3QBQ | pdb_00003qbq

Crystal structure of extracellular domains of mouse RANK-RANKL 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)
C	d3qbqc_	All beta proteins	TNF-like	TNF-like	TNF-like	TRANCE/RANKL cytokine	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3qbqa_	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)
C	SCOP2B Superfamily	TNF-like	8032348	3000061	SCOP2B (2022-06-29)
A	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)
D	TNFR_c6	e3qbqD2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6	ECOD (1.6)
D	TNFRSF11A_1st	e3qbqD1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF11A_1st	ECOD (1.6)
D	TNFRSF11A_2nd	e3qbqD3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF11A_2nd	ECOD (1.6)
B	TNFR_c6	e3qbqB2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6	ECOD (1.6)
B	TNFRSF11A_1st	e3qbqB1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF11A_1st	ECOD (1.6)
B	TNFRSF11A_2nd	e3qbqB3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF11A_2nd	ECOD (1.6)
C	TNF	e3qbqC1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
A	TNF	e3qbqA1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
B	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
C	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		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, D	PF18278	Receptor activator of the NF-KB cysteine-rich repeat domain 2 (RANK_CRD_2)	Receptor activator of the NF-KB cysteine-rich repeat domain 2	This domain is found in the receptor activator of the NF-KB (RANK) present in Mus musculus. RANK and its cognate ligand RANKL play a role in bone remodelling, immune function and mammary gland development in conjunction with various cytokines and hor ...	This domain is found in the receptor activator of the NF-KB (RANK) present in Mus musculus. RANK and its cognate ligand RANKL play a role in bone remodelling, immune function and mammary gland development in conjunction with various cytokines and hormones. The binding of RANKL to RANK causes trimerisation of the receptor, which activates the signalling pathway and results in osteoclastogenesis from progenitor cells and the activation of mature osteoclasts receptor activator of the NF-KB. This domain is the second of four cysteine rich pseudo-repeat domains (CRDs) and so is known as CRD2. RANK moves via a hinge region between CRD2 and CRD3 to make close contact with RANKL [1].	Domain
B, D	PF00020	TNFR/NGFR cysteine-rich region (TNFR_c6)	TNFR/NGFR cysteine-rich region		Domain
A, C	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, D	Tumor necrosis factor receptor superfamily member 11A	protein binding binding cytokine binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity tumor necrosis factor receptor activity death receptor activity cation binding ion binding metal ion binding small molecule binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation 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 cellular process positive regulation of signaling 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 immune response adaptive immune response 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 myeloid leukocyte differentiation cellular developmental process hemopoiesis cell development multinuclear osteoclast differentiation myeloid cell differentiation cell differentiation osteoclast differentiation leukocyte differentiation response to peptide response to chemical response to cytokine response to interleukin-1 acute-phase response regulation of localization 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 cell-cell signaling 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 response to alcohol response to oxygen-containing compound response to ethanol positive regulation of JNK cascade JNK cascade regulation of JNK cascade response to nutrient levels response to zinc ion starvation cellular response to starvation response to metal ion starvation cellular response to nutrient levels cellular response to stress response to starvation cellular response to zinc ion starvation response to mechanical stimulus response to abiotic stimulus response to hormone response to endogenous stimulus response to peptide hormone response to insulin response to nitrogen compound ossification cell surface receptor signaling pathway cytokine-mediated signaling pathway cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus response to tumor necrosis factor rhythmic process circadian rhythm circadian temperature homeostasis 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 biological process involved in interspecies interaction between organisms response to lipid response to other organism response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin mammary gland development gland development mammary gland lobule development mammary gland alveolus development regulation of leukocyte differentiation regulation of developmental process regulation of cell differentiation positive regulation of osteoclast differentiation regulation of cell development positive regulation of developmental process regulation of osteoclast differentiation positive regulation of cell differentiation positive regulation of hemopoiesis regulation of immune system process positive regulation of immune system process regulation of multicellular organismal development regulation of myeloid cell differentiation positive regulation of cell development regulation of myeloid leukocyte differentiation positive regulation of myeloid leukocyte differentiation positive regulation of myeloid cell differentiation regulation of hemopoiesis positive regulation of leukocyte differentiation	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane intracellular anatomical structure cytoplasm cytosol membrane microdomain membrane raft
A, C	Tumor necrosis factor ligand superfamily member 11	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity cytokine activity cytokine receptor binding tumor necrosis factor receptor superfamily binding tumor necrosis factor receptor binding identical protein binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation 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 cellular process positive regulation of signaling 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 anatomical structure morphogenesis animal organ morphogenesis 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 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 skeletal system development bone development tooth eruption odontogenesis cell-cell signaling paracrine signaling acute-phase response regulation of localization 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 myeloid leukocyte differentiation regulation of leukocyte differentiation cellular developmental process regulation of developmental process cell development regulation of cell differentiation regulation of cell development regulation of osteoclast differentiation cell differentiation osteoclast differentiation regulation of immune system process regulation of multicellular organismal development hemopoiesis regulation of myeloid cell differentiation regulation of myeloid leukocyte differentiation myeloid cell differentiation regulation of hemopoiesis leukocyte differentiation 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 response to chemical mononuclear cell migration myeloid leukocyte migration cell migration cell motility leukocyte chemotaxis locomotion ossification cell surface receptor signaling pathway response to cytokine cytokine-mediated signaling pathway response to peptide cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus 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 positive regulation of developmental process positive regulation of immune system process regulation of osteoclast development positive regulation of cell development osteoclast development positive regulation of myeloid leukocyte differentiation positive regulation of osteoclast differentiation positive regulation of cell differentiation positive regulation of hemopoiesis bone cell development positive regulation of osteoclast development myeloid cell development positive regulation of myeloid cell differentiation 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 amide transport 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 extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR022323	Tumour necrosis factor receptor 11	Family
B, D	IPR053075	Tumor necrosis factor receptor superfamily member 11A	Family
B, D	IPR022361	Tumour necrosis factor receptor 11A	Family
B, D	IPR001368	TNFR/NGFR cysteine-rich region	Domain
B, D	IPR041648	Rank, cysteine-rich repeat domain 2	Domain
B, D	IPR034040	Tumor necrosis factor receptor 11A, N-terminal	Domain
A, C	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
A, C	IPR006052	Tumour necrosis factor domain	Domain
A, C	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.