4E4D | pdb_00004e4d

Crystal structure of mouse 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth X]	d4e4dx_	All beta proteins	TNF-like	TNF-like	TNF-like	TRANCE/RANKL cytokine	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth X]	SCOP2B Superfamily	TNF-like	8032348	3000061	SCOP2B (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 R]		e4e4dR1	A: Lipocalins/Streptavidin	X: Enterocin 7A and 7B	H: Enterocin 7A and 7B	T: TIL	F:	ECOD (20:10:01)
A [auth X]		e4e4dX1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: FtsJ	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth R]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
A [auth X]	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 R]	PF00020	TNFR/NGFR cysteine-rich region (TNFR_c6)	TNFR/NGFR cysteine-rich region		Domain
A [auth X]	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 R]	Tumor necrosis factor receptor superfamily member 11B	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 negative regulation of tissue remodeling homeostatic process negative regulation of bone remodeling regulation of bone remodeling tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption negative regulation of bone resorption multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis 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 multicellular organism development 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 receptor complex cellular anatomical structure extracellular region cell periphery extracellular matrix external encapsulating structure extracellular space
A [auth X]	Tumor necrosis factor ligand superfamily member 11, soluble form	protein binding binding signaling receptor binding cytokine receptor binding tumor necrosis factor receptor superfamily binding identical protein binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity cytokine activity tumor necrosis factor receptor 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 developmental process immune system development multicellular organism development multicellular organismal process lymph node development immune system process animal organ development anatomical structure development hematopoietic or lymphoid organ development system development regulation of biosynthetic process positive regulation of biological 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 positive regulation of cellular process skeletal system development bone development positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette regulation of signaling positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication positive regulation of signaling inorganic ion homeostasis chemical homeostasis homeostatic process monoatomic ion homeostasis calcium ion homeostasis monoatomic cation homeostasis ossification cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway response to tumor necrosis factor cell population proliferation 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 bone remodeling tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis positive regulation of multicellular organismal process regulation of multicellular organismal process positive regulation of bone resorption myeloid leukocyte differentiation cellular developmental process hemopoiesis cell development osteoclast development myeloid cell differentiation cell differentiation bone cell development osteoclast differentiation myeloid cell development leukocyte differentiation regulation of localization nitrogen compound transport regulation of hormone secretion regulation of peptide secretion transport positive regulation of secretion by cell hormone secretion corticotropin-releasing hormone secretion localization peptide secretion secretion by cell regulation of secretion by cell positive regulation of hormone secretion positive regulation of secretion signal release regulation of biological quality regulation of peptide hormone secretion positive regulation of peptide secretion secretion regulation of transport regulation of hormone levels regulation of corticotropin-releasing hormone secretion positive regulation of peptide hormone secretion regulation of peptide transport cell-cell signaling export from cell positive regulation of corticotropin-releasing hormone secretion establishment of localization regulation of secretion peptide transport positive regulation of 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 positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction anatomical structure morphogenesis animal organ morphogenesis positive regulation of ERK1 and ERK2 cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade immune response tooth eruption odontogenesis 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 heat generation 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 regulation of fatty acid transport organic acid transport positive regulation of lipid transport lipid export from cell positive regulation of defense response temperature homeostasis regulation of acute inflammatory response regulation of fever generation inflammatory response prostaglandin transport regulation of defense response regulation of response to external stimulus positive regulation of heat generation regulation of lipid transport positive regulation of acute inflammatory response heat generation positive regulation of response to external stimulus icosanoid transport 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 icosanoid secretion acute inflammatory response fever generation organic anion transport defense response lipid localization positive regulation of lipid localization positive regulation of organic acid 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 phosphatidylinositol 3-kinase/protein kinase B signal transduction calcium-mediated signaling epithelium development mammary gland development gland development tissue development mammary gland epithelium development epithelial cell proliferation mammary gland epithelial cell proliferation regulation of leukocyte differentiation regulation of developmental process regulation of cell differentiation regulation of cell development regulation of osteoclast differentiation regulation of immune system process regulation of multicellular organismal development regulation of myeloid cell differentiation regulation of myeloid leukocyte differentiation regulation of hemopoiesis 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 regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction positive regulation of developmental process positive regulation of immune system process regulation of osteoclast development positive regulation of cell development positive regulation of myeloid leukocyte differentiation positive regulation of osteoclast differentiation positive regulation of cell differentiation positive regulation of hemopoiesis positive regulation of osteoclast development positive regulation of myeloid cell differentiation positive regulation of leukocyte differentiation 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	cellular anatomical structure intracellular anatomical structure cytoplasm extracellular region extracellular space cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

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

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.