2RTU

Solution structure of oxidized human HMGB1 A box

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2rtua1	All alpha proteins	HMG-box	HMG-box	HMG-box	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2rtua2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	HMG_box	e2rtuA1	A: alpha arrays	X: HMG-box (From Topology)	H: HMG-box (From Topology)	T: HMG-box	F: HMG_box	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF09011	HMG-box domain (HMG_box_2)	HMG-box domain	This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long ...	This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	High mobility group protein B1	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding supercoiled DNA binding DNA secondary structure binding four-way junction DNA binding bubble DNA binding modified amino acid binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding supercoiled DNA binding DNA secondary structure binding four-way junction DNA binding bubble DNA binding modified amino acid binding phospholipid binding lipid binding phosphatidylserine binding protein binding chemokine binding C-X-C chemokine binding cytokine binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding lipopolysaccharide binding carbohydrate derivative binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity lyase activity catalytic activity RNA binding damaged DNA binding transcription corepressor activity cell adhesion molecule binding protein-containing complex binding integrin binding cytokine activity RAGE receptor binding chemoattractant activity DNA binding, bending DNA polymerase binding enzyme binding single-stranded DNA binding	regulation of biological process regulation of restriction endodeoxyribonuclease activity regulation of cellular process regulation of catalytic activity biological regulation primary metabolic process regulation of macromolecule metabolic process DNA metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of molecular function regulation of endodeoxyribonuclease activity regulation of hydrolase activity regulation of deoxyribonuclease activity regulation of biological process regulation of restriction endodeoxyribonuclease activity regulation of cellular process regulation of catalytic activity biological regulation primary metabolic process regulation of macromolecule metabolic process DNA metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of molecular function regulation of endodeoxyribonuclease activity regulation of hydrolase activity regulation of deoxyribonuclease activity regulation of nuclease activity metabolic process cellular process macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA metabolic process positive regulation of molecular function regulation of DNA binding regulation of binding positive regulation of binding positive regulation of DNA binding multicellular organismal 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 interleukin-1 production 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 positive regulation of cytokine production 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 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 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 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 interleukin-8 production interleukin-8 production regulation of interleukin-8 production positive regulation of JNK cascade JNK cascade intracellular signaling cassette positive regulation of MAPK cascade regulation of JNK cascade regulation of MAPK cascade MAPK cascade cell chemotaxis chemotaxis dendritic cell chemotaxis leukocyte migration dendritic cell migration cellular response to chemical stimulus taxis response to chemical mononuclear cell migration cell migration cell motility leukocyte chemotaxis locomotion negative regulation of locomotion regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration negative regulation of biological process negative regulation of endothelial cell migration negative regulation of blood vessel endothelial cell migration regulation of locomotion regulation of cell migration negative regulation of cellular process blood vessel endothelial cell migration regulation of endothelial cell migration negative regulation of cell motility negative regulation of cell migration negative regulation of transcription initiation by RNA polymerase II transcription preinitiation complex assembly negative regulation of RNA biosynthetic process cellular component biogenesis 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 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 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 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 negative regulation of biosynthetic process regulation of transcription initiation by RNA polymerase II negative regulation of DNA-templated transcription initiation inflammatory response inflammatory response to antigenic stimulus 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 vascular endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation positive regulation of vascular endothelial cell proliferation positive regulation of monocyte chemotaxis positive regulation of locomotion positive regulation of chemotaxis positive regulation of cell migration regulation of monocyte chemotaxis positive regulation of cell motility 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 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 mismatch repair regulation of cellular response to stress positive regulation of mismatch repair positive regulation of DNA repair cellular response to stress DNA repair positive regulation of nucleobase-containing compound metabolic process regulation of DNA repair positive regulation of DNA metabolic process DNA damage response regulation of mismatch repair 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 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 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 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 positive regulation of ERK1 and ERK2 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 interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production 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 interleukin-12 production interleukin-12 production positive regulation of interleukin-12 production DNA recombination regulation of leukocyte activation regulation of alpha-beta T cell 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 regulation of leukocyte cell-cell adhesion negative regulation of lymphocyte differentiation negative regulation of CD4-positive, alpha-beta T cell differentiation negative regulation of leukocyte activation regulation of alpha-beta T cell differentiation regulation of CD4-positive, 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 regulation of cell-cell adhesion negative regulation of cell differentiation 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 positive regulation of blood vessel endothelial cell migration positive regulation of endothelial cell migration chromatin organization chromatin remodeling heterochromatin formation epigenetic regulation of gene expression negative regulation of gene expression, epigenetic DNA ligation regulation of DNA ligation positive regulation of DNA ligation myeloid dendritic cell activation myeloid leukocyte activation T-helper 1 cell activation 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 double-strand break repair 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 membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle endoplasmic reticulum-Golgi intermediate compartment cytoplasm cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane membrane protein complex alphav-beta3 integrin-HMGB1 complex membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle endoplasmic reticulum-Golgi intermediate compartment cytoplasm intracellular membrane-bounded organelle extracellular region extracellular space membraneless organelle intracellular membraneless organelle chromosome condensed chromosome cell surface membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule endomembrane system intracellular organelle lumen organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle vesicle nucleus nucleoplasm nuclear lumen endosome vesicle lumen cytoplasmic vesicle lumen secretory granule lumen transcription regulator complex transcription repressor complex endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017967	HMG box A DNA-binding domain, conserved site	Conserved Site
A	IPR036910	High mobility group box domain superfamily	Homologous Superfamily
A	IPR050342	High Mobility Group Box (HMGB)	Family
A	IPR009071	High mobility group box domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	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 multiple organ dysfunction syndrome breast cancer drug-induced liver injury

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.