6Z3G

Repulsive Guidance Molecule A (RGMA) in complex with Growth Differentiation Factor 5 (GDF5)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d6z3ga_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	automated matches	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	SCOP2B Superfamily	Cystine-knot cytokines	8070313	3000846	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)
A	PF00019	e6z3gA1	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	PF06535	e6z3gB1	A: alpha bundles	X: Spectrin repeat-like	H: Repulsive guidance molecule (RGM) N-terminal domain (From Topology)	T: Repulsive guidance molecule (RGM) N-terminal domain	F: PF06535	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00019	Transforming growth factor beta like domain (TGF_beta)	Transforming growth factor beta like domain	-	Domain
B	PF06535	Repulsive guidance molecule (RGM) N-terminus (RGM_N)	Repulsive guidance molecule (RGM) N-terminus	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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	Repulsive guidance molecule A	molecular transducer activity coreceptor activity signaling receptor activity transferrin receptor binding protein binding binding signaling receptor binding	regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization cellular developmental process cell projection organization positive regulation of biological process cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization cellular developmental process cell projection organization positive regulation of biological process cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development cell differentiation anatomical structure development positive regulation of cell projection organization cellular component organization or biogenesis positive regulation of cellular process system development developmental process regulation of biological process plasma membrane bounded cell projection organization regulation of cell projection organization biological regulation nervous system development generation of neurons neuron development cellular process regulation of plasma membrane bounded cell projection organization embryonic epithelial tube formation chordate embryonic development tube formation embryo development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching epithelial tube morphogenesis morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure cellular response to stimulus cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of signal transduction cell communication cellular response to endogenous stimulus signal transduction BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus regulation of signaling regulation of BMP signaling pathway cell surface receptor signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus response to BMP regulation of response to stimulus regulation of cell communication transforming growth factor beta receptor superfamily signaling pathway response to growth factor regulation of growth axonogenesis regulation of cellular component size developmental growth negative regulation of biological process regulation of cell differentiation regulation of neurogenesis regulation of cell development cell projection morphogenesis negative regulation of growth neuron projection morphogenesis regulation of biological quality negative regulation of cellular component organization negative regulation of cell growth developmental growth involved in morphogenesis negative regulation of axonogenesis negative regulation of developmental growth negative regulation of multicellular organismal process regulation of collateral sprouting regulation of developmental process plasma membrane bounded cell projection morphogenesis cell growth cell morphogenesis regulation of nervous system development negative regulation of neurogenesis regulation of extent of cell growth regulation of axonogenesis negative regulation of cellular process negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of cell size regulation of multicellular organismal development collateral sprouting regulation of developmental growth developmental cell growth negative regulation of developmental process growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation negative regulation of neuron projection development negative regulation of cell development negative regulation of collateral sprouting regulation of anatomical structure size regulation of cellular response to stress negative regulation of neuron projection regeneration regeneration neuron projection regeneration response to wounding regulation of axon regeneration response to external stimulus negative regulation of response to external stimulus regulation of neuron projection regeneration negative regulation of axon regeneration regulation of response to external stimulus response to axon injury regulation of response to wounding cellular response to stress axon regeneration response to stress regulation of response to stress negative regulation of response to stimulus negative regulation of response to wounding catabolic process positive regulation of protein metabolic process positive regulation of membrane protein ectodomain proteolysis positive regulation of cellular metabolic process macromolecule catabolic process regulation of primary metabolic process cellular catabolic process positive regulation of metabolic process organic substance metabolic process regulation of proteolysis proteolysis membrane protein proteolysis positive regulation of macromolecule metabolic process protein metabolic process membrane protein ectodomain proteolysis organonitrogen compound catabolic process regulation of membrane protein ectodomain proteolysis organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process primary metabolic process regulation of cellular metabolic process regulation of catabolic process regulation of macromolecule metabolic process protein catabolic process positive regulation of protein catabolic process positive regulation of catabolic process positive regulation of proteolysis regulation of cellular catabolic process positive regulation of cellular catabolic process metabolic process macromolecule metabolic process regulation of metabolic process organic substance catabolic process regulation of protein catabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process 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 organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	membrane cellular anatomical entity side of membrane cell surface cell periphery plasma membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR029034	Cystine-knot cytokine	Homologous Superfamily
A	IPR015615	Transforming growth factor-beta-related	Family
A	IPR017948	Transforming growth factor beta, conserved site	Conserved Site
A	IPR001111	TGF-beta, propeptide	Domain
A	IPR001839	Transforming growth factor-beta, C-terminal	Domain
B	IPR010536	Repulsive guidance molecule, N-terminal	Domain
B	IPR009496	Repulsive guidance molecule, C-terminal	Domain
B	IPR040287	Repulsive guidance molecule	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	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
B	Pharos: Q96B86	astrocytic tumor ductal breast carcinoma in situ malignant glioma pancreatic intraductal papillary-mucinous carcinoma breast cancer glioblastoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast carcinoma invasive ductal breast carcinoma oligodendroglioma psoriasis

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.