3URF | pdb_00003urf

Human RANKL/OPG complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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	d3urfa_	All beta proteins	TNF-like	TNF-like	TNF-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	TNF-like	8064716	4000294	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TNF-like	8064717	3000061	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth Z]	Pyr_redox_dim	e3urfZ6	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: Pyr_redox_dim	ECOD (v294.1)
A	Tubulin	e3urfA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: SH3	T: SH3	F: Tubulin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth Z]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
A	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth Z]	PF00020	TNFR/NGFR cysteine-rich region (TNFR_c6)	TNFR/NGFR cysteine-rich region		Domain
A	PF00229	TNF(Tumour Necrosis Factor) family (TNF)	TNF(Tumour Necrosis Factor) family		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth Z]	Tumor necrosis factor receptor superfamily member 11B	molecular transducer activity signaling receptor activity molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity glycosaminoglycan binding organic acid binding binding ion binding heparan sulfate binding anion binding molecular transducer activity signaling receptor activity molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity glycosaminoglycan binding organic acid binding binding ion binding heparan sulfate binding anion binding carboxylic acid binding carbohydrate derivative binding small molecule binding sulfur compound binding	developmental process multicellular organismal process regulation of biological process regulation of animal organ morphogenesis regulation of developmental process regulation of odontogenesis of dentin-containing tooth negative regulation of developmental process regulation of odontogenesis odontogenesis of dentin-containing tooth odontogenesis animal organ development biological regulation negative regulation of biological process negative regulation of odontogenesis anatomical structure morphogenesis developmental process multicellular organismal process regulation of biological process regulation of animal organ morphogenesis regulation of developmental process regulation of odontogenesis of dentin-containing tooth negative regulation of developmental process regulation of odontogenesis odontogenesis of dentin-containing tooth odontogenesis animal organ development biological regulation negative regulation of biological process negative regulation of odontogenesis anatomical structure morphogenesis negative regulation of odontogenesis of dentin-containing tooth anatomical structure development animal organ morphogenesis negative regulation of animal organ morphogenesis regulation of multicellular organismal process negative regulation of multicellular organismal process regulation of anatomical structure morphogenesis multicellular organism development skeletal system development system development cellular component organization extracellular matrix organization cellular process cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization apoptotic process cell death programmed cell death myeloid leukocyte differentiation regulation of leukocyte differentiation regulation of cellular process cellular developmental process cell development regulation of cell differentiation regulation of cell development regulation of osteoclast differentiation cell differentiation osteoclast differentiation negative regulation of cellular process regulation of immune system process negative regulation of cell differentiation negative regulation of hemopoiesis regulation of multicellular organismal development negative regulation of leukocyte differentiation hemopoiesis regulation of myeloid cell differentiation regulation of myeloid leukocyte differentiation negative regulation of myeloid cell differentiation negative regulation of osteoclast differentiation negative regulation of myeloid leukocyte differentiation negative regulation of cell development myeloid cell differentiation negative regulation of immune system process immune system process regulation of hemopoiesis leukocyte differentiation cellular response to stimulus response to stimulus signaling signal transduction cell communication negative regulation of signaling response to cytokine regulation of signal transduction negative regulation of cell communication cytokine-mediated signaling pathway cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus regulation of signaling cell surface receptor signaling pathway regulation of tumor necrosis factor-mediated signaling pathway negative regulation of response to stimulus regulation of cytokine-mediated signaling pathway negative regulation of tumor necrosis factor-mediated signaling pathway negative regulation of signal transduction response to peptide regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus regulation of response to stimulus negative regulation of cytokine-mediated signaling pathway response to chemical regulation of cell communication response to tumor necrosis factor	protein-containing complex signaling receptor complex cellular anatomical structure extracellular region cell periphery plasma membrane membrane extracellular matrix external encapsulating structure
A	Tumor necrosis factor ligand superfamily member 11, soluble form	molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity protein binding binding signaling receptor binding cytokine receptor binding tumor necrosis factor receptor superfamily binding tumor necrosis factor receptor binding identical protein binding	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical cellular process cellular response to cytokine stimulus cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical cellular process cellular response to cytokine stimulus signal transduction positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling positive regulation of ERK1 and ERK2 cascade positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade immune response immune system process phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process developmental process anatomical structure morphogenesis tooth eruption anatomical structure development odontogenesis animal organ development animal organ morphogenesis cell-cell signaling paracrine signaling regulation of programmed cell death extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of programmed cell death regulation of apoptotic process positive regulation of extrinsic apoptotic signaling pathway cell death positive regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway apoptotic process programmed cell death regulation of apoptotic signaling pathway acute-phase response regulation of localization multicellular organismal process regulation of heat generation localization regulation of prostaglandin secretion monocarboxylic acid transport fatty acid transport positive regulation of inflammatory response prostaglandin secretion positive regulation of icosanoid secretion carboxylic acid transport lipid transport response to external stimulus regulation of inflammatory response establishment of localization regulation of fatty acid transport regulation of secretion organic acid transport positive regulation of lipid transport lipid export from cell positive regulation of defense response temperature homeostasis regulation of acute inflammatory response positive regulation of multicellular organismal process regulation of fever generation inflammatory response prostaglandin transport regulation of defense response regulation of response to external stimulus transport homeostatic process positive regulation of heat generation regulation of lipid transport positive regulation of secretion by cell positive regulation of acute inflammatory response heat generation regulation of secretion by cell secretion by cell positive regulation of response to external stimulus positive regulation of secretion icosanoid transport signal release regulation of icosanoid secretion response to stress regulation of response to stress positive regulation of prostaglandin secretion positive regulation of fever generation by positive regulation of prostaglandin secretion positive regulation of fever generation regulation of multicellular organismal process icosanoid secretion acute inflammatory response fever generation organic anion transport regulation of transport secretion defense response export from cell lipid localization positive regulation of lipid localization positive regulation of organic acid transport multicellular organismal-level homeostasis positive regulation of transport regulation of lipid localization macromolecule localization regulation of organic acid transport positive regulation of fatty acid transport regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction calcium-mediated signaling epithelium development cell population proliferation mammary gland development gland development tissue development mammary gland epithelium development epithelial cell proliferation mammary gland epithelial cell proliferation positive regulation of JNK cascade JNK cascade regulation of JNK cascade inorganic ion homeostasis chemical homeostasis monoatomic ion homeostasis calcium ion homeostasis monoatomic cation homeostasis cell chemotaxis chemotaxis monocyte chemotaxis leukocyte migration cellular response to chemical stimulus taxis mononuclear cell migration myeloid leukocyte migration cell migration cell motility leukocyte chemotaxis locomotion ossification regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway response to tumor necrosis factor osteoclast proliferation leukocyte proliferation regulation of homotypic cell-cell adhesion positive regulation of cell adhesion regulation of cell adhesion homotypic cell-cell adhesion positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion positive regulation of homotypic cell-cell adhesion regulation of cell-cell adhesion regulation of leukocyte differentiation regulation of cell differentiation regulation of cell development positive regulation of developmental process multicellular organism development skeletal system development cell differentiation regulation of immune system process positive regulation of immune system process regulation of osteoclast development system development positive regulation of cell development regulation of myeloid leukocyte differentiation osteoclast development positive regulation of myeloid leukocyte differentiation leukocyte differentiation myeloid leukocyte differentiation cellular developmental process regulation of developmental process cell development positive regulation of osteoclast differentiation regulation of osteoclast differentiation positive regulation of cell differentiation positive regulation of hemopoiesis bone cell development osteoclast differentiation bone development positive regulation of osteoclast development regulation of multicellular organismal development hemopoiesis regulation of myeloid cell differentiation myeloid cell differentiation myeloid cell development positive regulation of myeloid cell differentiation regulation of hemopoiesis positive regulation of leukocyte differentiation regulation of bone remodeling tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption tissue remodeling bone remodeling anatomical structure homeostasis positive regulation of bone resorption nitrogen compound transport regulation of hormone secretion regulation of peptide secretion hormone secretion corticotropin-releasing hormone secretion peptide secretion positive regulation of hormone secretion regulation of biological quality regulation of peptide hormone secretion positive regulation of peptide secretion regulation of hormone levels regulation of corticotropin-releasing hormone secretion positive regulation of peptide hormone secretion regulation of peptide transport positive regulation of corticotropin-releasing hormone secretion peptide transport peptide hormone secretion hormone transport negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process 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 leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of lymphocyte activation positive regulation of cell activation T cell activation positive regulation of leukocyte activation positive regulation of T cell activation cell activation regulation of T cell activation regulation of leukocyte cell-cell adhesion regulation of lymphocyte activation mammary gland lobule development mammary gland alveolus development response to leukemia inhibitory factor cellular response to leukemia inhibitory factor	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth Z]	IPR011029	Death-like domain superfamily	Homologous Superfamily
B [auth Z]	IPR022323	Tumour necrosis factor receptor 11	Family
B [auth Z]	IPR017371	Tumour necrosis factor receptor 11B	Family
B [auth Z]	IPR057633	Tumor necrosis factor receptor superfamily member 11B, Death domain	Domain
B [auth Z]	IPR052459	Tumor necrosis factor receptor superfamily decoy receptor	Family
B [auth Z]	IPR000488	Death domain	Domain
B [auth Z]	IPR001368	TNFR/NGFR cysteine-rich region	Domain
A	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
A	IPR006052	Tumour necrosis factor domain	Domain
A	IPR017355	Tumour necrosis factor ligand 10/11	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth Z]	Pharos: O00300	rheumatoid arthritis hypercalcemia disease osteoporosis juvenile Paget disease Arthritis, Experimental uremia lung cancer lytic metastatic bone lesion malignant mesothelioma pilocytic astrocytoma Crohn disease interstitial cystitis lung carcinoma malignant ependymoma malignant pancreatic neoplasm rheumatoid arthritis hypercalcemia disease osteoporosis juvenile Paget disease Arthritis, Experimental uremia lung cancer lytic metastatic bone lesion malignant mesothelioma pilocytic astrocytoma Crohn disease interstitial cystitis lung carcinoma malignant ependymoma malignant pancreatic neoplasm osteosarcoma atypical teratoid rhabdoid tumor pituitary cancer bone resorption disease glioblastoma malignant glioma ovarian cancer bone Paget disease congestive heart failure ulcerative colitis
A	Pharos: O14788	osteopetrosis osteoporosis hypercalcemia disease B-cell chronic lymphocytic leukemia autosomal recessive osteopetrosis 2 Alveolar Bone Loss autosomal dominant osteopetrosis 2 lung cancer malignant pancreatic neoplasm osteonecrosis osteosarcoma pancreatic intraductal papillary-mucinous neoplasm pituitary cancer breast disease primary biliary cholangitis osteopetrosis osteoporosis hypercalcemia disease B-cell chronic lymphocytic leukemia autosomal recessive osteopetrosis 2 Alveolar Bone Loss autosomal dominant osteopetrosis 2 lung cancer malignant pancreatic neoplasm osteonecrosis osteosarcoma pancreatic intraductal papillary-mucinous neoplasm pituitary cancer breast disease primary biliary cholangitis ulcerative colitis hypothyroidism arthritic joint disease ovarian cancer autosomal recessive osteopetrosis periodontitis bone giant cell tumor cancer root resorption vitiligo Crohn disease Hashimoto thyroiditis lytic metastatic bone lesion nasopharyngeal carcinoma autoimmune disease pancreatic intraductal papillary-mucinous carcinoma periodontitis, chronic, adult breast cancer postmenopausal osteoporosis chronic periodontitis tuberculosis cystic fibrosis

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.