6Z3J | pdb_00006z3j

Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) (crystal form 1)

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)
B	d6z3jb_	Small proteins	Cystine-knot cytokines	Cystine-knot cytokines	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6z3ja_	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)
D	SCOP2B Superfamily	RGM family, N-terminal helical domain	8107356	3002873	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RGM family, N-terminal helical domain	8107356	3002873	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cystine-knot cytokines	8070313	3000846	SCOP2B (2022-06-29)
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)
D	RGM_N_N	e6z3jD1	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: RGM_N_N	ECOD (1.6)
C	RGM_N_N	e6z3jC1	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: RGM_N_N	ECOD (1.6)
B	TGF_beta	e6z3jB1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: TGF_beta	ECOD (1.6)
A	TGF_beta	e6z3jA1	A: few secondary structure elements	X: Cystine-knot cytokines (From Topology)	H: Cystine-knot cytokines (From Topology)	T: Cystine-knot cytokines	F: TGF_beta	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF06535	Repulsive guidance molecule (RGM) N-terminal domain (RGM_N)	Repulsive guidance molecule (RGM) N-terminal domain	This entry represents the small N-terminal three helical bundle domain found at the N-terminus of proteins in the Repulsive Guidance Molecule (RGM) family, which is involved in various functions related to nervous system development and signaling. Me ...	This entry represents the small N-terminal three helical bundle domain found at the N-terminus of proteins in the Repulsive Guidance Molecule (RGM) family, which is involved in various functions related to nervous system development and signaling. Members of this family act as bone morphogenetic protein (BMP) coreceptors, enhancing BMP signaling pathways. They play crucial roles in regulating neural tube closure, inhibiting neurite outgrowth, and promoting neuronal adhesion. Additionally, they are involved in the regulation of iron homeostasis through the modulation of hepcidin expression. The RGM family also influences axon guidance and synapse formation, contributing to the patterning of the developing nervous system.	Domain
A, B	PF00019	Transforming growth factor beta like domain (TGF_beta)	Transforming growth factor beta like domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	RGM domain family member B	molecular transducer activity coreceptor activity signaling receptor activity identical protein binding protein binding binding	cellular response to stimulus cellular response to BMP stimulus regulation of biological process cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus biological regulation cell communication cellular response to endogenous stimulus response to BMP cellular response to stimulus cellular response to BMP stimulus regulation of biological process cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus biological regulation cell communication cellular response to endogenous stimulus response to BMP cellular process transforming growth factor beta receptor superfamily signaling pathway signal transduction response to growth factor BMP signaling pathway enzyme-linked receptor protein signaling pathway cell adhesion positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process	cellular anatomical structure membrane side of membrane cell periphery plasma membrane membrane microdomain membrane raft membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle endoplasmic reticulum-Golgi intermediate compartment cytoplasm intracellular membrane-bounded organelle
A, 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 cellular anatomical structure plasma membrane membrane extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: Q6NW40	rheumatoid arthritis prostate cancer adrenoleukodystrophy colorectal adenoma gastric carcinoma lung carcinoma oligodendroglioma atopic eczema colorectal cancer hydrolethalus syndrome malignant ependymoma pancreatic intraductal papillary-mucinous neoplasm Prostatic Neoplasms atypical teratoid rhabdoid tumor cystic fibrosis rheumatoid arthritis prostate cancer adrenoleukodystrophy colorectal adenoma gastric carcinoma lung carcinoma oligodendroglioma atopic eczema colorectal cancer hydrolethalus syndrome malignant ependymoma pancreatic intraductal papillary-mucinous neoplasm Prostatic Neoplasms atypical teratoid rhabdoid tumor cystic fibrosis interstitial cystitis medulloblastoma pilocytic astrocytoma psoriasis
A, 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 R01GM157729.