1S55 | pdb_00001s55

Mouse RANKL Structure at 1.9A Resolution

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	d1s55c_	All beta proteins	TNF-like	TNF-like	TNF-like	TRANCE/RANKL cytokine	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d1s55b_	All beta proteins	TNF-like	TNF-like	TNF-like	TRANCE/RANKL cytokine	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1s55a_	All beta proteins	TNF-like	TNF-like	TNF-like	TRANCE/RANKL cytokine	house 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)
B	SCOP2B Superfamily	TNF-like	8032348	3000061	SCOP2B (2022-06-29)
A	SCOP2 Family	TNF-like	8019968	4000294	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TNF-like	8032348	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)
C	TNF	e1s55C1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
B	TNF	e1s55B1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
A	TNF	e1s55A1	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)
C	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	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
A, B, 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
A, B, 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
A, B, C	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
A, B, C	IPR006052	Tumour necrosis factor domain	Domain
A, B, 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.