3EVS

Crystal structure of the GDF-5:BMP receptor IB 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 [auth B]	d3evsb_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d3evsc_	Small proteins	Snake toxin-like	Snake toxin-like	automated matches	automated matches	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 B]	SCOP2B Superfamily	Cystine-knot cytokines	8070313	3000846	SCOP2B (2022-06-29)
B [auth C]	SCOP2 Family	Extracellular domain of cell surface receptors	8080448	4003329	SCOP2 (2022-06-29)
B [auth C]	SCOP2 Superfamily	Snake toxin-like	8080449	3000545	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)
A [auth B]	PF00019	e3evsB1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: PF00019	ECOD (1.6)
B [auth C]	PF01064	e3evsC1	A: few secondary structure elements	X: Snake toxin-like (From Topology)	H: Snake toxin-like (From Topology)	T: Snake toxin-like	F: PF01064	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	2.10.90.10	Mainly Beta	Ribbon	Cystine Knot Cytokines, subunit B	Cystine-knot cytokines	CATH (4.3.0)
B [auth C]	2.10.60.10	Mainly Beta	Ribbon	CD59	CD59	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF00019	Transforming growth factor beta like domain (TGF_beta)	Transforming growth factor beta like domain	-	Domain
B [auth C]	PF01064	Activin types I and II receptor domain (Activin_recp)	Activin types I and II receptor domain	This Pfam entry consists of both TGF-beta receptor types. This is an alignment of the hydrophilic cysteine-rich ligand-binding domains, Both receptor types, (type I and II) posses a 9 amino acid cysteine box, with the the consensus CCX{4-5}CN. The t ...	This Pfam entry consists of both TGF-beta receptor types. This is an alignment of the hydrophilic cysteine-rich ligand-binding domains, Both receptor types, (type I and II) posses a 9 amino acid cysteine box, with the the consensus CCX{4-5}CN. The type I receptors also possess 7 extracellular residues preceding the cysteine box.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Growth/differentiation factor 5	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity BMP binding cytokine binding cytokine activity identical protein binding	cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 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 cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 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 enzyme-linked receptor protein signaling pathway positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway biological regulation positive regulation of intracellular signal transduction positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway SMAD protein signal transduction regulation of response to stimulus regulation of cell communication cellular process regulation of SMAD protein signal transduction positive regulation of SMAD protein signal transduction positive regulation of signaling cellular response to BMP stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to endogenous stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway response to growth factor BMP signaling pathway developmental process multicellular organismal process cellular developmental process connective tissue development animal organ development tissue development chondroblast differentiation multicellular organism development skeletal system development cell differentiation anatomical structure development cartilage development system development cell-cell signaling regulation of cartilage development regulation of chondrocyte differentiation regulation of developmental process regulation of cell differentiation positive regulation of chondrocyte differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of multicellular organismal process regulation of multicellular organismal development chondrocyte differentiation positive regulation of multicellular organismal process positive regulation of cartilage development neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of neuron apoptotic process limb development appendage development embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development anatomical structure morphogenesis appendage morphogenesis limb morphogenesis regulation of multicellular organism growth regulation of growth regulation of developmental growth developmental growth growth multicellular organism growth ossification tissue remodeling bone remodeling ossification involved in bone remodeling positive regulation of BMP signaling pathway regulation of BMP signaling pathway regulation of cellular response to growth factor stimulus response to mechanical stimulus response to abiotic stimulus response to external stimulus positive regulation of neuron differentiation neurogenesis neuron differentiation nervous system development generation of neurons regulation of neuron differentiation negative regulation of mesenchymal cell apoptotic process mesenchymal cell apoptotic process regulation of mesenchymal cell apoptotic process forelimb morphogenesis negative regulation of cartilage development negative regulation of chondrocyte differentiation negative regulation of cell differentiation negative regulation of developmental process negative regulation of multicellular organismal process negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation hindlimb morphogenesis cellular response to transforming growth factor beta stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway	cell periphery plasma membrane membrane cellular anatomical entity extracellular region extracellular space
B [auth C]	Bone morphogenetic protein receptor type-1B	BMP binding protein binding binding cytokine binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding BMP binding protein binding binding cytokine binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane receptor protein serine/threonine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity transforming growth factor beta receptor activity cation binding metal ion binding SMAD binding BMP receptor activity transforming growth factor beta receptor activity, type I	developmental process multicellular organismal process cellular developmental process connective tissue development animal organ development cell development tissue development multicellular organism development skeletal system development cell differentiation chondrocyte differentiation anatomical structure development cellular process chondrocyte development developmental process multicellular organismal process cellular developmental process connective tissue development animal organ development cell development tissue development multicellular organism development skeletal system development cell differentiation chondrocyte differentiation anatomical structure development cellular process chondrocyte development cartilage development system development regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process sensory organ development eye development retina development in camera-type eye visual system development camera-type eye development sensory system development dorsal/ventral pattern formation pattern specification process regionalization bone development regulation of developmental process regulation of biomineral tissue development regulation of bone mineralization positive regulation of ossification positive regulation of developmental process positive regulation of biomineral tissue development ossification biomineral tissue development regulation of multicellular organismal process regulation of multicellular organismal development bone mineralization positive regulation of bone mineralization positive regulation of multicellular organismal process regulation of ossification cell aggregation cartilage condensation anatomical structure morphogenesis skeletal system morphogenesis animal organ morphogenesis phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process regulation of hormone levels steroid metabolic process estrogen biosynthetic process lipid biosynthetic process primary metabolic process hormone metabolic process estrogen metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of biological quality steroid biosynthetic process hormone biosynthetic process steroid hormone biosynthetic process lipid metabolic process ovulation cycle rhythmic process reproductive process multicellular organismal reproductive process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA biosynthetic process endochondral bone morphogenesis bone morphogenesis cellular response to stimulus cellular response to growth factor stimulus cell surface receptor protein serine/threonine kinase signaling pathway response to stimulus cell surface receptor signaling pathway signaling cellular response to transforming growth factor beta stimulus response to endogenous stimulus cell communication cellular response to endogenous stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway signal transduction enzyme-linked receptor protein signaling pathway regulation of cartilage development positive regulation of cartilage development osteoblast differentiation negative regulation of cell population proliferation cell population proliferation negative regulation of biological process negative regulation of chondrocyte proliferation regulation of cell population proliferation negative regulation of cellular process chondrocyte proliferation cellular response to BMP stimulus response to BMP BMP signaling pathway axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cellular component organization or biogenesis plasma membrane bounded cell projection organization axon guidance nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron projection guidance neuron development retinal ganglion cell axon guidance central nervous system neuron differentiation central nervous system development regulation of chondrocyte differentiation regulation of cell differentiation positive regulation of chondrocyte differentiation positive regulation of cell differentiation positive regulation of cell communication extrinsic apoptotic signaling pathway via death domain receptors positive regulation of signal transduction regulation of signal transduction regulation of programmed cell death extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of response to stimulus regulation of signaling positive regulation of extrinsic apoptotic signaling pathway via death domain receptors 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 regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway via death domain receptors regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway positive regulation of signaling carbohydrate derivative biosynthetic process proteoglycan biosynthetic process organonitrogen compound metabolic process organonitrogen compound biosynthetic process glycoprotein biosynthetic process carbohydrate derivative metabolic process glycoprotein metabolic process protein metabolic process proteoglycan metabolic process regulation of osteoblast differentiation positive regulation of osteoblast differentiation defense response response to stress inflammatory response ovulation cycle process sexual reproduction developmental growth sex differentiation cellular process involved in reproduction in multicellular organism development of primary female sexual characteristics female gamete generation developmental process involved in reproduction gamete generation development of primary sexual characteristics ovarian cumulus expansion reproductive structure development ovarian follicle development mammalian oogenesis stage gonad development reproductive system development female gonad development oogenesis growth female sex differentiation fused antrum stage antral ovarian follicle growth germ cell development	somatodendritic compartment cell projection dendrite dendritic tree neuron projection cellular anatomical entity plasma membrane bounded cell projection protein-containing complex receptor complex cell body neuronal cell body cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A [auth B]	IPR015615	Transforming growth factor-beta-related	Family
A [auth B]	IPR017948	Transforming growth factor beta, conserved site	Conserved Site
A [auth B]	IPR001111	TGF-beta, propeptide	Domain
A [auth B]	IPR001839	Transforming growth factor-beta, C-terminal	Domain
B [auth C]	IPR000472	Activin types I and II receptor domain	Domain
B [auth C]	IPR000719	Protein kinase domain	Domain
B [auth C]	IPR003605	GS domain	Domain
B [auth C]	IPR000333	Ser/Thr protein kinase, TGFB receptor	Family
B [auth C]	IPR017441	Protein kinase, ATP binding site	Binding Site
B [auth C]	IPR045860	Snake toxin-like superfamily	Homologous Superfamily
B [auth C]	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
B [auth C]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B [auth C]	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B]	Pharos: P43026	fibular hypoplasia and complex brachydactyly multiple synostoses syndrome 2 acromesomelic dysplasia, Hunter-Thompson type osteoarthritis symphalangism, proximal, 1B acromesomelic dysplasia, Grebe type brachydactyly type C proximal symphalangism brachydactyly type A1C brachydactyly type A2 rheumatoid arthritis developmental dysplasia of the hip 1 calcaneonavicular coalition brachydactyly Hip Dislocation, Congenital fibular hypoplasia and complex brachydactyly multiple synostoses syndrome 2 acromesomelic dysplasia, Hunter-Thompson type osteoarthritis symphalangism, proximal, 1B acromesomelic dysplasia, Grebe type brachydactyly type C proximal symphalangism brachydactyly type A1C brachydactyly type A2 rheumatoid arthritis developmental dysplasia of the hip 1 calcaneonavicular coalition brachydactyly Hip Dislocation, Congenital malignant mesothelioma osteoarthritis susceptibility 5 acromesomelic dysplasia osteogenesis imperfecta atypical teratoid rhabdoid tumor skin carcinoma intellectual disability multiple synostoses syndrome osteoarthritis, knee osteosarcoma proximal symphalangism 1A bone development disease brachydactyly type A1 large cell medulloblastoma multiple synostoses syndrome 1 osteoarthritis susceptibility 1 polydactyly angel-shaped phalango-epiphyseal dysplasia brachydactyly type A1A

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 R01GM133198.