4BQ7 | pdb_00004bq7

Crystal structure of the RGMB-Neo1 complex form 2

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	von Willebrand factor type D domain-like	8107357	3002872	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	von Willebrand factor type D domain-like	8107357	3002872	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	fn3	e4bq7A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: fn3	ECOD (1.6)
A	fn3_6	e4bq7A2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: fn3_6	ECOD (1.6)
B	fn3	e4bq7B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: fn3	ECOD (1.6)
B	fn3_6	e4bq7B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: fn3_6	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, F	PF06534	Repulsive guidance molecule (RGM) C-terminal domain (RGM_C)	Repulsive guidance molecule (RGM) C-terminal domain	This entry represents the C-terminal VWD like domain found at the C-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 fami ...	This entry represents the C-terminal VWD like domain found at the C-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	PF00041	Fibronectin type III domain (fn3)	Fibronectin type III domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, F	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
C, E	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	NEOGENIN	molecular transducer activity signaling receptor activity protein binding binding BMP receptor binding receptor serine/threonine kinase binding signaling receptor binding transmembrane receptor protein serine/threonine kinase binding cell adhesion molecule binding cadherin binding co-receptor binding	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of protein transport regulation of localization establishment of protein localization nitrogen compound transport intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis negative regulation of protein transport regulation of localization establishment of protein localization nitrogen compound transport regulation of cellular process regulation of protein localization transport negative regulation of biological process negative regulation of transport protein localization to extracellular region localization regulation of secretion by cell secretion by cell negative regulation of secretion negative regulation of cellular process negative regulation of secretion by cell intracellular protein localization negative regulation of protein localization regulation of biological process regulation of transport secretion biological regulation regulation of establishment of protein localization establishment of protein localization to extracellular region negative regulation of establishment of protein localization export from cell regulation of protein transport protein secretion establishment of localization regulation of protein secretion regulation of secretion negative regulation of protein secretion protein transport macromolecule localization cellular process multicellular organismal-level iron ion homeostasis multicellular organismal process multicellular organismal-level homeostasis multicellular organismal-level chemical homeostasis trans-synaptic signaling regulation of signaling trans-synaptic signaling, modulating synaptic transmission signaling modulation of chemical synaptic transmission cell-cell signaling cell communication chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway positive regulation of signal transduction cellular response to growth factor stimulus response to stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of biological process regulation of signal transduction positive regulation of BMP signaling pathway positive regulation of response to stimulus cellular response to endogenous stimulus signal transduction BMP signaling pathway enzyme-linked receptor protein signaling pathway positive regulation of cellular process cellular response to BMP stimulus cell surface receptor signaling pathway regulation of BMP signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway response to BMP regulation of response to stimulus transforming growth factor beta receptor superfamily signaling pathway response to growth factor positive regulation of signaling cell projection organization regulation of cellular response to stress negative regulation of neuron projection regeneration neuron projection development regeneration neuron projection regeneration multicellular organism development neuron differentiation cell differentiation anatomical structure development response to wounding system development developmental process regulation of axon regeneration negative regulation of cellular component organization regulation of cell projection organization response to external stimulus nervous system development generation of neurons negative regulation of response to external stimulus regulation of neuron projection regeneration negative regulation of axon regeneration regulation of neuron projection development regulation of cellular component organization regulation of developmental process cellular developmental process regulation of response to external stimulus cell development response to axon injury regulation of response to wounding cellular component organization neurogenesis cellular response to stress axon regeneration regulation of response to stress response to stress cellular component organization or biogenesis negative regulation of cell projection organization plasma membrane bounded cell projection organization negative regulation of response to stimulus negative regulation of developmental process negative regulation of response to wounding axon development negative regulation of neuron projection development neuron development regulation of plasma membrane bounded cell projection organization RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic 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 regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cell adhesion myoblast fusion cell-cell fusion muscle cell differentiation myotube differentiation muscle structure development syncytium formation by plasma membrane fusion anatomical structure morphogenesis anatomical structure formation involved in morphogenesis syncytium formation striated muscle cell differentiation	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region cell surface growth cone axon cell projection distal axon neuron projection plasma membrane bounded cell projection site of polarized growth membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen glutamatergic synapse Golgi apparatus cytoplasm endomembrane system protein-containing complex plasma membrane protein complex membrane protein complex intracellular vesicle vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, F	IPR010536	Repulsive guidance molecule, N-terminal	Domain
D, F	IPR009496	Repulsive guidance molecule, C-terminal	Domain
D, F	IPR040287	Repulsive guidance molecule	Family
C, E	IPR010536	Repulsive guidance molecule, N-terminal	Domain
C, E	IPR009496	Repulsive guidance molecule, C-terminal	Domain
C, E	IPR040287	Repulsive guidance molecule	Family
A, B	IPR010560	Neogenin, C-terminal	Domain
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR003598	Immunoglobulin subtype 2	Domain
A, B	IPR003599	Immunoglobulin domain subtype	Domain
A, B	IPR013098	Immunoglobulin I-set	Domain
A, B	IPR003961	Fibronectin type III	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR007110	Immunoglobulin-like domain	Domain
A, B	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D, F	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
C, E	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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.