6CIJ | pdb_00006cij

Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G [auth N]	HMG_box	e6cijN1	A: alpha arrays	X: HMG-box (From Topology)	H: HMG-box (From Topology)	T: HMG-box	F: HMG_box	ECOD (1.6)
I [auth D]	RAG2	e6cijD1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: RAG2	ECOD (1.6)
J [auth B]	RAG2	e6cijB1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: RAG2	ECOD (1.6)
A	RAG1_1st	e6cijA1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RAG1_1st	ECOD (1.6)
A	RAG1_3rd	e6cijA3	A: alpha bundles	X: V(D)J recombination-activating protein 1 helical bundle domain (From Topology)	H: V(D)J recombination-activating protein 1 helical bundle domain (From Topology)	T: V(D)J recombination-activating protein 1 helical bundle domain	F: RAG1_3rd	ECOD (1.6)
A	RAG1_2nd	e6cijA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RAG1_2nd	ECOD (1.6)
B [auth C]	RAG1_1st	e6cijC1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RAG1_1st	ECOD (1.6)
B [auth C]	RAG1_3rd	e6cijC2	A: alpha bundles	X: V(D)J recombination-activating protein 1 helical bundle domain (From Topology)	H: V(D)J recombination-activating protein 1 helical bundle domain (From Topology)	T: V(D)J recombination-activating protein 1 helical bundle domain	F: RAG1_3rd	ECOD (1.6)
B [auth C]	RAG1_2nd	e6cijC3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RAG1_2nd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth N]	PF00505	HMG (high mobility group) box (HMG_box)	HMG (high mobility group) box		Domain
I [auth D], J [auth B]	PF03089	Recombination activating protein 2 (RAG2)	Recombination activating protein 2	-	Repeat
A, B [auth C]	PF26105	Recombination-activation protein 1 (RAG1) C-terminal domain (RAG1_C)	Recombination-activation protein 1 (RAG1) C-terminal domain	This entry represents the C-terminal domain of RAG1. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RAG1 mediates DNA-bi ...	This entry represents the C-terminal domain of RAG1. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS) [3]. Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerises with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerisation and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008 [4,5].	Domain
A, B [auth C]	PF26104	Recombination-activation protein 1 (RAG1) ZnH2 domain (RAG1_ZnH2)	Recombination-activation protein 1 (RAG1) ZnH2 domain	This entry represents the ZnH2 domain of RAG1. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RAG1 mediates DNA-binding ...	This entry represents the ZnH2 domain of RAG1. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS) [3]. Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerises with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerisation and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008 [4,5].	Domain
A, B [auth C]	PF26025	Recombination-activation protein 1 (RAG1) pre-RNase H domain (RAG1_pre-RNase_H)	Recombination-activation protein 1 (RAG1) pre-RNase H domain	This entry represents the pre-RNase H domain of RAG1. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RAG1 mediates DNA-b ...	This entry represents the pre-RNase H domain of RAG1. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS) [3]. Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerises with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerisation and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008 [4,5].	Domain
A, B [auth C]	PF26024	Recombination-activation protein 1 (RAG1) DNA-binding domain (RAG1_DNA-bd)	Recombination-activation protein 1 (RAG1) DNA-binding domain	This entry represents the dimerisation and DNA-binding domain of RAG1. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RA ...	This entry represents the dimerisation and DNA-binding domain of RAG1. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS) [3]. Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerises with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerisation and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008 [4,5].	Domain
A, B [auth C]	PF26101	Recombination-activation protein 1 (RAG1) ZnC2 domain (RAG1_ZnC2)	Recombination-activation protein 1 (RAG1) ZnC2 domain	This entry represents the ZnC2 domain of RAG1. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RAG1 mediates DNA-binding ...	This entry represents the ZnC2 domain of RAG1. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS) [3]. Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerises with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerisation and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008 [4,5].	Domain
A, B [auth C]	PF26100	Recombination-activation protein 1 (RAG1) RNase H domain (RAG1_RNase_H)	Recombination-activation protein 1 (RAG1) RNase H domain	This entry represents the catalytic RNase H domain of RAG1. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RAG1 mediates ...	This entry represents the catalytic RNase H domain of RAG1. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS) [3]. Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerises with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerisation and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008 [4,5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth F]	DNA (46-MER)	-	-	-
E [auth J]	DNA (5'-D(PCPTPGPGPAPTPCPTPGPGPCPCPTPGPTPCPTPTP*A)-3')	-	-	-
G [auth N]	High mobility group protein B1	DNA binding double-stranded DNA binding binding nucleic acid binding supercoiled DNA binding DNA secondary structure binding four-way junction DNA binding bubble DNA binding lipid binding lipopolysaccharide binding carbohydrate derivative binding enzyme regulator activity kinase activator activity enzyme activator activity DNA binding double-stranded DNA binding binding nucleic acid binding supercoiled DNA binding DNA secondary structure binding four-way junction DNA binding bubble DNA binding lipid binding lipopolysaccharide binding carbohydrate derivative binding enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding protein binding DNA-binding transcription factor binding calcium-dependent protein kinase regulator activity DNA binding, bending single-stranded DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA binding double-stranded RNA binding modified amino acid binding ion binding anion binding phospholipid binding phosphatidylserine binding small molecule binding chemokine binding C-X-C chemokine binding cytokine binding signaling receptor binding signaling receptor regulator activity receptor ligand activity signaling receptor activator activity RNA polymerase II-specific DNA-binding transcription factor binding transcription coactivator activity lyase activity catalytic activity single-stranded RNA binding damaged DNA binding cell adhesion molecule binding protein-containing complex binding integrin binding cytokine activity RAGE receptor binding chemoattractant activity DNA polymerase binding enzyme binding	multicellular organismal process regulation of cellular process interleukin-1 production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of interleukin-1 production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process multicellular organismal process regulation of cellular process interleukin-1 production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of interleukin-1 production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of interleukin-1 production biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process immune system development developmental process multicellular organism development immune system process anatomical structure development regulation of immune system process regulation of tolerance induction tolerance induction system development cellular response to stimulus positive regulation of cell communication positive regulation of response to biotic stimulus regulation of toll-like receptor 9 signaling pathway positive regulation of signal transduction pattern recognition receptor signaling pathway response to stimulus regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication immune response-activating signaling pathway positive regulation of immune response signal transduction positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of pattern recognition receptor signaling pathway immune response response to other organism regulation of innate immune response response to external stimulus positive regulation of intracellular signal transduction regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response toll-like receptor 9 signaling pathway activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus intracellular receptor signaling pathway signaling regulation of cytoplasmic pattern recognition receptor signaling pathway positive regulation of response to stimulus endolysosomal toll-like receptor signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of intracellular signal transduction regulation of response to stress response to stress innate immune response response to external biotic stimulus positive regulation of toll-like receptor 9 signaling pathway regulation of signaling positive regulation of innate immune response defense response defense response to symbiont regulation of cell communication positive regulation of signaling cellular component organization organelle organization DNA geometric change chromosome organization DNA conformation change cellular component organization or biogenesis catabolic process autophagy process utilizing autophagic mechanism regulation of leukocyte differentiation cellular developmental process regulation of developmental process cell development mononuclear cell differentiation regulation of cell differentiation regulation of cell development positive regulation of developmental process positive regulation of hemopoiesis positive regulation of cell differentiation cell differentiation regulation of multicellular organismal development hemopoiesis positive regulation of cell development regulation of dendritic cell differentiation regulation of hemopoiesis dendritic cell differentiation positive regulation of leukocyte differentiation positive regulation of dendritic cell differentiation leukocyte differentiation adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte activation lymphocyte differentiation cell activation involved in immune response CD4-positive, alpha-beta T cell differentiation CD4-positive, alpha-beta T cell differentiation involved in immune response alpha-beta T cell differentiation involved in immune response leukocyte activation alpha-beta T cell differentiation T cell activation involved in immune response alpha-beta T cell activation involved in immune response T cell activation CD4-positive, alpha-beta T cell activation leukocyte activation involved in immune response alpha-beta T cell activation T cell differentiation lymphocyte activation involved in immune response T-helper cell differentiation cell activation T cell differentiation involved in immune response T-helper 1 type immune response adaptive immune response immune effector process T-helper 1 cell differentiation positive regulation of interleukin-8 production interleukin-8 production regulation of interleukin-8 production negative regulation of transcription initiation by RNA polymerase II transcription preinitiation complex assembly negative regulation of biological process regulation of primary metabolic process negative regulation of RNA biosynthetic process cellular component biogenesis nucleobase-containing compound metabolic process DNA-templated transcription regulation of DNA-templated transcription initiation regulation of RNA metabolic process cellular component assembly transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of cellular component organization negative regulation of transcription by RNA polymerase II negative regulation of metabolic process primary metabolic process negative regulation of protein-containing complex assembly negative regulation of macromolecule biosynthetic process RNA polymerase II preinitiation complex assembly regulation of DNA-templated transcription negative regulation of RNA metabolic process regulation of RNA polymerase II transcription preinitiation complex assembly regulation of cellular component organization negative regulation of RNA polymerase II transcription preinitiation complex assembly RNA metabolic process protein-DNA complex organization RNA biosynthetic process nucleic acid biosynthetic process regulation of protein-containing complex assembly protein-containing complex assembly negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process protein-containing complex organization protein-DNA complex assembly nucleobase-containing compound biosynthetic process regulation of cellular component biogenesis DNA-templated transcription initiation nucleic acid metabolic process negative regulation of biosynthetic process regulation of transcription initiation by RNA polymerase II negative regulation of DNA-templated transcription initiation cell population proliferation positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of vascular endothelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation vascular endothelial cell proliferation epithelial cell proliferation positive regulation of vascular endothelial cell proliferation interleukin-10 production regulation of interleukin-10 production positive regulation of interleukin-10 production regulation of type II interferon production type II interferon production negative regulation of type II interferon production negative regulation of cytokine production negative regulation of gene expression negative regulation of multicellular organismal process positive regulation of viral life cycle positive regulation of viral process viral life cycle modulation by symbiont of entry into host biological process involved in interaction with host biological process involved in symbiotic interaction regulation of viral entry into host cell regulation of viral life cycle regulation of viral process symbiont entry into host cell viral process symbiont entry into host positive regulation of viral entry into host cell positive regulation by symbiont of entry into host regulation of biological process involved in symbiotic interaction localization import into cell transport phagocytosis apoptotic cell clearance endocytosis establishment of localization vesicle-mediated transport positive regulation of autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process interferon-alpha production regulation of interferon-alpha production positive regulation of type I interferon production type I interferon production positive regulation of interferon-alpha production regulation of type I interferon production myeloid cell differentiation immune response-regulating cell surface receptor signaling pathway cell surface toll-like receptor signaling pathway immune response-activating cell surface receptor signaling pathway regulation of toll-like receptor 4 signaling pathway positive regulation of toll-like receptor 4 signaling pathway innate immune response activating cell surface receptor signaling pathway cell surface pattern recognition receptor signaling pathway cell surface receptor signaling pathway toll-like receptor 4 signaling pathway positive regulation of ERK1 and ERK2 cascade intracellular signaling cassette positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade lymphocyte mediated immunity regulation of immune effector process T cell mediated immunity immune response to tumor cell regulation of response to tumor cell T cell mediated immune response to tumor cell regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of T cell mediated immune response to tumor cell leukocyte mediated immunity regulation of T cell mediated immunity response to tumor cell regulation of adaptive immune response regulation of immune response to tumor cell regulation of leukocyte mediated immunity regulation of lymphocyte mediated immunity regulation of localization negative regulation of transport negative regulation of endocytosis negative regulation of phagocytosis regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport negative regulation of apoptotic cell clearance regulation of apoptotic cell clearance regulation of myeloid cell differentiation positive regulation of myeloid cell differentiation regulation of interleukin-12 production interleukin-12 production positive regulation of interleukin-12 production regulation of interferon-beta production interferon-beta production positive regulation of interferon-beta production DNA recombination DNA metabolic process carbohydrate metabolic process glucan catabolic process energy derivation by oxidation of organic compounds glycogen metabolic process carbohydrate catabolic process generation of precursor metabolites and energy macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process polysaccharide catabolic process energy reserve metabolic process myeloid progenitor cell differentiation hematopoietic progenitor cell differentiation positive regulation of locomotion regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration positive regulation of cell migration positive regulation of blood vessel endothelial cell migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of cell motility regulation of cell migration blood vessel endothelial cell migration regulation of endothelial cell migration cell migration cell motility locomotion regulation of cellular response to stress cellular response to stress nucleotide-excision repair DNA repair regulation of DNA repair DNA damage response regulation of nucleotide-excision repair regulation of DNA metabolic process chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression heterochromatin organization negative regulation of gene expression, epigenetic regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction regulation of sprouting angiogenesis angiogenesis regulation of vasculature development tube morphogenesis positive regulation of sprouting angiogenesis regulation of anatomical structure morphogenesis blood vessel development blood vessel morphogenesis tube development positive regulation of angiogenesis sprouting angiogenesis vasculature development circulatory system development anatomical structure morphogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis myeloid dendritic cell activation myeloid leukocyte activation inflammatory response regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production homeostatic process neutrophil clearance neutrophil homeostasis multicellular organismal-level homeostasis leukocyte homeostasis homeostasis of number of cells myeloid cell homeostasis regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding positive regulation of binding positive regulation of DNA binding positive regulation of response to wounding wound healing regulation of response to wounding positive regulation of wound healing regulation of wound healing response to wounding monosaccharide metabolic process regulation of generation of precursor metabolites and energy regulation of polysaccharide metabolic process positive regulation of glycogen metabolic process regulation of small molecule metabolic process regulation of glycogen catabolic process small molecule metabolic process positive regulation of glycogen catabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process regulation of carbohydrate catabolic process hexose metabolic process positive regulation of glucose metabolic process positive regulation of carbohydrate metabolic process positive regulation of small molecule metabolic process regulation of glycogen metabolic process glucose metabolic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death DNA topological change regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production interleukin-1 beta production chemokine (C-X-C motif) ligand 2 production regulation of chemokine (C-X-C motif) ligand 2 production positive regulation of chemokine (C-X-C motif) ligand 2 production regulation of chemokine production chemokine production positive regulation of chemokine production positive regulation of JNK cascade JNK cascade regulation of JNK cascade macrophage activation involved in immune response myeloid cell activation involved in immune response macrophage activation cell chemotaxis chemotaxis dendritic cell chemotaxis leukocyte migration dendritic cell migration cellular response to chemical stimulus taxis response to chemical mononuclear cell migration leukocyte chemotaxis negative regulation of locomotion negative regulation of endothelial cell migration negative regulation of blood vessel endothelial cell migration negative regulation of cell motility negative regulation of cell migration inflammatory response to antigenic stimulus positive regulation of monocyte chemotaxis positive regulation of chemotaxis regulation of monocyte chemotaxis myeloid leukocyte migration positive regulation of mononuclear cell migration regulation of mononuclear cell migration regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of leukocyte migration positive regulation of leukocyte chemotaxis regulation of chemotaxis monocyte chemotaxis base-excision repair mismatch repair positive regulation of mismatch repair positive regulation of DNA repair positive regulation of DNA metabolic process regulation of mismatch repair positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of myeloid progenitor cell differentiation positive regulation of myeloid progenitor cell differentiation regulation of hematopoietic progenitor cell differentiation positive regulation of hematopoietic progenitor cell differentiation plasma membrane bounded cell projection organization cell projection organization neuron projection development nervous system development generation of neurons neurogenesis neuron differentiation neuron development positive regulation of cytosolic calcium ion concentration regulation of biological quality endothelial cell chemotaxis plasmacytoid dendritic cell activation interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production regulation of toll-like receptor 2 signaling pathway positive regulation of toll-like receptor 2 signaling pathway toll-like receptor 2 signaling pathway animal organ development respiratory tube development lung development respiratory system development response to lipid cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to biotic stimulus response to bacterium cellular response to lipid response to molecule of bacterial origin regulation of monocyte chemotactic protein-1 production positive regulation of monocyte chemotactic protein-1 production monocyte chemotactic protein-1 production response to corticosteroid response to hormone response to steroid hormone response to endogenous stimulus response to glucocorticoid regulation of alpha-beta T cell activation regulation of leukocyte activation regulation of cell activation negative regulation of cell adhesion negative regulation of T cell differentiation negative regulation of hemopoiesis negative regulation of leukocyte differentiation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of CD4-positive, alpha-beta T cell activation negative regulation of cell-cell adhesion negative regulation of lymphocyte differentiation regulation of leukocyte cell-cell adhesion negative regulation of CD4-positive, alpha-beta T cell differentiation negative regulation of leukocyte activation regulation of CD4-positive, alpha-beta T cell differentiation regulation of alpha-beta T cell differentiation negative regulation of alpha-beta T cell differentiation negative regulation of lymphocyte activation leukocyte cell-cell adhesion regulation of T cell differentiation cell adhesion cell-cell adhesion negative regulation of cell differentiation regulation of cell-cell adhesion regulation of lymphocyte differentiation negative regulation of developmental process regulation of cell adhesion regulation of T cell activation negative regulation of cell activation negative regulation of cell development regulation of CD4-positive, alpha-beta T cell activation negative regulation of immune system process negative regulation of alpha-beta T cell activation regulation of lymphocyte activation positive regulation of cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of leukocyte proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of activated T cell proliferation mononuclear cell proliferation positive regulation of leukocyte proliferation regulation of activated T cell proliferation positive regulation of leukocyte cell-cell adhesion leukocyte proliferation activated T cell proliferation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of mononuclear cell proliferation T cell proliferation regulation of lymphocyte proliferation positive regulation of cell adhesion regulation of T cell proliferation regulation of mononuclear cell proliferation sensory organ development eye development visual system development sensory system development T-helper 1 cell activation double-strand break repair response to peptide response to interleukin-7 response to cytokine cellular response to cytokine stimulus cellular response to interleukin-7 double-strand break repair via nonhomologous end joining somatic cell DNA recombination V(D)J recombination somatic diversification of immune receptors via germline recombination within a single locus somatic diversification of immune receptors	cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane membrane protein complex alphav-beta3 integrin-HMGB1 complex extracellular region extracellular space cell surface membrane-bounded organelle vesicle lumen intracellular anatomical structure cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane membrane protein complex alphav-beta3 integrin-HMGB1 complex extracellular region extracellular space cell surface membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen organelle secretory granule secretory vesicle cytoplasm vesicle cell projection neuron projection plasma membrane bounded cell projection endoplasmic reticulum-Golgi intermediate compartment membraneless organelle intracellular membraneless organelle chromosome condensed chromosome ficolin-1-rich granule ficolin-1-rich granule lumen nucleus nucleoplasm nuclear lumen early endosome endosome transcription regulator complex transcription repressor complex endoplasmic reticulum
H [auth L]	DNA (30-MER)	-	-	-
I [auth D], J [auth B]	V(D)J recombination-activating protein 2	binding phospholipid binding lipid binding phosphatidylinositol binding phosphatidylinositol-3,5-bisphosphate binding ion binding anion binding phosphatidylinositol bisphosphate binding phosphatidylinositol phosphate binding small molecule binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity binding phospholipid binding lipid binding phosphatidylinositol binding phosphatidylinositol-3,5-bisphosphate binding ion binding anion binding phosphatidylinositol bisphosphate binding phosphatidylinositol phosphate binding small molecule binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding sequence-specific DNA binding DNA binding nucleic acid binding phosphatidylinositol-4,5-bisphosphate binding phosphatidylinositol-3,4-bisphosphate binding phosphatidylinositol-3,4,5-trisphosphate binding cation binding transition metal ion binding zinc ion binding metal ion binding	multicellular organismal process cell population proliferation homeostatic process B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation B cell homeostatic proliferation leukocyte activation mononuclear cell proliferation immune system process lymphocyte proliferation cellular process multicellular organismal process cell population proliferation homeostatic process B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation B cell homeostatic proliferation leukocyte activation mononuclear cell proliferation immune system process lymphocyte proliferation cellular process developmental process cellular developmental process hemopoiesis cell development mononuclear cell differentiation lymphocyte differentiation B cell differentiation cell differentiation anatomical structure development leukocyte differentiation B cell lineage commitment cell fate commitment defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus T cell activation T cell differentiation nucleobase-containing compound metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process T cell differentiation in thymus mature B cell differentiation B cell activation involved in immune response cell activation involved in immune response leukocyte activation involved in immune response lymphocyte activation involved in immune response mature B cell differentiation involved in immune response immune response immune effector process T cell lineage commitment regulation of biological process regulation of growth regulation of developmental growth regulation of developmental process developmental growth positive regulation of organ growth growth biological regulation positive regulation of biological process organ growth positive regulation of developmental process positive regulation of growth regulation of organ growth positive regulation of multicellular organismal process regulation of multicellular organismal process positive regulation of developmental growth regulation of leukocyte differentiation regulation of cellular process regulation of leukocyte activation negative regulation of biological process regulation of cell activation negative regulation of T cell differentiation in thymus regulation of cell differentiation regulation of cell development negative regulation of cell adhesion multicellular organism development negative regulation of T cell differentiation regulation of immune system process negative regulation of hemopoiesis negative regulation of leukocyte differentiation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of cell-cell adhesion negative regulation of lymphocyte differentiation regulation of leukocyte cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation regulation of T cell differentiation in thymus negative regulation of lymphocyte activation leukocyte cell-cell adhesion regulation of T cell differentiation cell adhesion cell-cell adhesion negative regulation of cellular process negative regulation of cell differentiation regulation of cell-cell adhesion regulation of lymphocyte differentiation regulation of multicellular organismal development negative regulation of developmental process regulation of cell adhesion regulation of T cell activation negative regulation of cell activation negative regulation of cell development negative regulation of immune system process regulation of hemopoiesis regulation of lymphocyte activation immature B cell differentiation pre-B cell allelic exclusion pre-B cell differentiation regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process immune system development somatic cell DNA recombination V(D)J recombination somatic diversification of immune receptors via germline recombination within a single locus somatic diversification of immune receptors system development	protein-containing complex DNA recombinase complex protein-DNA complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle protein-containing complex DNA recombinase complex protein-DNA complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen
K [auth M]	DNA (41-MER)	-	-	-
F [auth G]	DNA (60-MER)	-	-	-
D [auth I]	DNA (5'-D(GPAPTPCPTPGPGPCPCPTPGPTPCPTPTPA)-3')	-	-	-
A, B [auth C]	V(D)J recombination-activating protein 1	protein binding binding histone binding hydrolase activity catalytic activity sequence-specific DNA binding DNA binding nucleic acid binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity protein binding binding histone binding hydrolase activity catalytic activity sequence-specific DNA binding DNA binding nucleic acid binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity ubiquitin-protein transferase activity identical protein binding protein homodimerization activity protein dimerization activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development cellular process leukocyte differentiation immune system development animal organ development gland development hematopoietic or lymphoid organ development multicellular organism development thymus development system development response to stimulus immune response adaptive immune response regulation of defense response regulation of biological process behavioral fear response defense response regulation of fear response biological regulation multicellular organismal response to stress regulation of behavioral fear response regulation of behavior behavior behavioral defense response fear response regulation of response to stimulus regulation of response to stress response to stress regulation of multicellular organismal process protein autoubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal multicellular organismal-level homeostasis leukocyte homeostasis T cell homeostasis homeostatic process homeostasis of number of cells lymphocyte homeostasis regulation of leukocyte differentiation regulation of cellular process regulation of developmental process regulation of leukocyte activation regulation of cell activation regulation of cell differentiation regulation of cell development regulation of T cell differentiation T cell activation T cell differentiation regulation of immune system process regulation of lymphocyte differentiation regulation of multicellular organismal development regulation of T cell activation regulation of hemopoiesis regulation of lymphocyte activation response to light stimulus system process learning learning or memory nervous system process visual learning visual behavior cognition associative learning response to radiation response to abiotic stimulus nucleobase-containing compound metabolic process DNA recombination DNA metabolic process nucleic acid metabolic process T cell differentiation in thymus regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process negative regulation of programmed cell death leukocyte apoptotic process regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of T cell apoptotic process lymphocyte apoptotic process negative regulation of apoptotic process negative regulation of leukocyte apoptotic process negative regulation of cellular process regulation of T cell apoptotic process T cell apoptotic process apoptotic process programmed cell death negative regulation of lymphocyte apoptotic process immature B cell differentiation pre-B cell allelic exclusion pre-B cell differentiation regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of thymocyte apoptotic process thymocyte apoptotic process regulation of thymocyte apoptotic process positive regulation of T cell differentiation positive regulation of developmental process positive regulation of cell activation positive regulation of leukocyte activation positive regulation of immune system process positive regulation of T cell activation positive regulation of cell development regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process positive regulation of biological process positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of hemopoiesis positive regulation of cell differentiation regulation of cell-cell adhesion positive regulation of cellular process positive regulation of cell adhesion regulation of cell adhesion positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation cellular component organization chromatin organization cellular component organization or biogenesis somatic cell DNA recombination V(D)J recombination somatic diversification of immune receptors via germline recombination within a single locus somatic diversification of immune receptors	protein-containing complex DNA recombinase complex protein-DNA complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle protein-containing complex DNA recombinase complex protein-DNA complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen catalytic complex endodeoxyribonuclease complex intracellular protein-containing complex endonuclease complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth N]	IPR036910	High mobility group box domain superfamily	Homologous Superfamily
G [auth N]	IPR050342	High Mobility Group Box (HMGB)	Family
G [auth N]	IPR017967	HMG box A DNA-binding domain, conserved site	Conserved Site
G [auth N]	IPR009071	High mobility group box domain	Domain
I [auth D], J [auth B]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
I [auth D], J [auth B]	IPR011043	Galactose oxidase/kelch, beta-propeller	Homologous Superfamily
I [auth D], J [auth B]	IPR015915	Kelch-type beta-propeller	Homologous Superfamily
I [auth D], J [auth B]	IPR025162	Recombination activating protein 2, PHD domain	Domain
I [auth D], J [auth B]	IPR004321	V-D-J recombination activating protein 2	Family
A, B [auth C]	IPR024627	V(D)J recombination-activating protein 1	Family
A, B [auth C]	IPR058552	V(D)J recombination-activating protein 1, DNA-binding domain	Domain
A, B [auth C]	IPR019485	V(D)J recombination-activating protein 1, Zinc finger	Domain
A, B [auth C]	IPR058553	V(D)J recombination-activating protein 1, pre-RNase H domain	Domain
A, B [auth C]	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
A, B [auth C]	IPR023336	RAG nonamer-binding domain	Domain
A, B [auth C]	IPR058557	V(D)J recombination-activating protein 1, C-terminal domain	Domain
A, B [auth C]	IPR018957	Zinc finger, C3HC4 RING-type	Domain
A, B [auth C]	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A, B [auth C]	IPR058558	V(D)J recombination-activating protein 1, RING finger, HC subclass	Domain
A, B [auth C]	IPR058556	V(D)J recombination-activating protein 1, ZnH2 domain	Domain
A, B [auth C]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B [auth C]	IPR035714	RAG1 importin-binding	Domain
A, B [auth C]	IPR058555	V(D)J recombination-activating protein 1, ZnC2 domain	Domain
A, B [auth C]	IPR001841	Zinc finger, RING-type	Domain
A, B [auth C]	IPR058554	V(D)J recombination-activating protein 1, RNase H domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
G [auth N]	Pharos: P09429	esophageal squamous cell carcinoma pulmonary fibrosis Inflammation extrahepatic cholestasis neuropathy, painful neuralgia leukostasis myocardial infarction gestational trophoblastic neoplasm ovarian cancer rheumatoid arthritis acute lymphoblastic leukemia lung adenocarcinoma Burkitt lymphoma myocardial ischemia esophageal squamous cell carcinoma pulmonary fibrosis Inflammation extrahepatic cholestasis neuropathy, painful neuralgia leukostasis myocardial infarction gestational trophoblastic neoplasm ovarian cancer rheumatoid arthritis acute lymphoblastic leukemia lung adenocarcinoma Burkitt lymphoma myocardial ischemia pancreatic ductal adenocarcinoma psoriasis juvenile idiopathic arthritis bone osteosarcoma mycosis fungoides coronary artery disease psoriatic arthritis idiopathic interstitial pneumonia breast cancer multiple organ dysfunction syndrome drug-induced liver injury