7NDG | pdb_00007ndg

Cryo-EM structure of the ternary complex between Netrin-1, Neogenin and Repulsive Guidance Molecule B

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)
C [auth F]	SCOP2B Superfamily	von Willebrand factor type D domain-like	8107357	3002872	SCOP2B (2022-06-29)
K [auth I]	SCOP2B Superfamily	von Willebrand factor type D domain-like	8107357	3002872	SCOP2B (2022-06-29)
E [auth C]	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)
B	fn3	e7ndgB1	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	e7ndgB2	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)
G [auth H]	fn3	e7ndgH3	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)
G [auth H]	fn3_6	e7ndgH2	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)
J [auth E]	fn3	e7ndgE1	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)
J [auth E]	fn3_6	e7ndgE3	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)
C [auth F]	RGM_N_C	e7ndgF1	A: beta barrels	X: Repulsive guidance molecule (RGM) family (From Topology)	H: Repulsive guidance molecule (RGM) family (From Topology)	T: Repulsive guidance molecule (RGM) family	F: RGM_N_C	ECOD (1.6)
K [auth I]	RGM_N_C	e7ndgI1	A: beta barrels	X: Repulsive guidance molecule (RGM) family (From Topology)	H: Repulsive guidance molecule (RGM) family (From Topology)	T: Repulsive guidance molecule (RGM) family	F: RGM_N_C	ECOD (1.6)
E [auth C]	RGM_N_C	e7ndgC1	A: beta barrels	X: Repulsive guidance molecule (RGM) family (From Topology)	H: Repulsive guidance molecule (RGM) family (From Topology)	T: Repulsive guidance molecule (RGM) family	F: RGM_N_C	ECOD (1.6)
A	Laminin_N	e7ndgA3	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Laminin_N	ECOD (1.6)
A	Laminin_EGF_1	e7ndgA2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF_1	ECOD (1.6)
A	Laminin_EGF	e7ndgA4	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF	ECOD (1.6)
A	Laminin_EGF_2	e7ndgA1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF_2	ECOD (1.6)
F [auth G]	Laminin_N	e7ndgG1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Laminin_N	ECOD (1.6)
F [auth G]	Laminin_EGF_1	e7ndgG4	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF_1	ECOD (1.6)
F [auth G]	Laminin_EGF	e7ndgG2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF	ECOD (1.6)
F [auth G]	Laminin_EGF_2	e7ndgG3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF_2	ECOD (1.6)
I [auth D]	Laminin_N	e7ndgD3	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Laminin_N	ECOD (1.6)
I [auth D]	Laminin_EGF_1	e7ndgD4	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF_1	ECOD (1.6)
I [auth D]	Laminin_EGF	e7ndgD2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF	ECOD (1.6)
I [auth D]	Laminin_EGF_2	e7ndgD1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF_2	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, G [auth H], J [auth E]	PF00041	Fibronectin type III domain (fn3)	Fibronectin type III domain		Domain
C [auth F], E [auth C], K [auth I]	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, F [auth G], I [auth D]	PF24973	Laminin/attractin EGF domain (EGF_LMN_ATRN)	Laminin/attractin EGF domain	This entry represents the EGF-like domains found in laminin subunits (alpha, beta, gamma), attractin (ATRN), netrin, among others. ATRN is involved in the initial immune cell clustering during inflammatory response and may regulate chemotactic activi ...	This entry represents the EGF-like domains found in laminin subunits (alpha, beta, gamma), attractin (ATRN), netrin, among others. ATRN is involved in the initial immune cell clustering during inflammatory response and may regulate chemotactic activity of chemokines. It may play a role in melanocortin signaling pathways that regulate energy homeostasis and hair color [1]. It was thought to have dipeptidase activity but it was shown later to lack that activity [2]. Laminins are crucial for the formation of stable basement membranes and organising receptor complexes and cytoskeletal components. Netrins control guidance of central nervous system commissural axons and peripheral motor axons, serving as survival factors and regulating apoptosis.	Domain
A, F [auth G], I [auth D]	PF00053	Laminin EGF domain (EGF_laminin)	Laminin EGF domain	This family is like Pfam:PF00008 but has 8 conserved cysteines instead of six.	Domain
A, F [auth G], I [auth D]	PF00055	Laminin N-terminal (Domain VI) (Laminin_N)	Laminin N-terminal (Domain VI)		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, G [auth H], J [auth E]	Neogenin	-	cell adhesion cellular process	cell periphery cellular anatomical structure plasma membrane membrane
C [auth F], E [auth C], K [auth I]	Repulsive Guidance Molecule B (C-terminal region)	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
D [auth N], H [auth M], L [auth O]	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, F [auth G], I [auth D]	Netrin-1	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity	developmental process ear morphogenesis embryonic organ morphogenesis multicellular organismal process ear development sensory organ development animal organ development embryonic morphogenesis embryo development multicellular organism development anatomical structure morphogenesis sensory organ morphogenesis inner ear development inner ear morphogenesis anatomical structure development developmental process ear morphogenesis embryonic organ morphogenesis multicellular organismal process ear development sensory organ development animal organ development embryonic morphogenesis embryo development multicellular organism development anatomical structure morphogenesis sensory organ morphogenesis inner ear development inner ear morphogenesis anatomical structure development animal organ morphogenesis embryonic organ development axon extension regulation of growth regulation of cellular process axonogenesis regulation of cellular component size developmental growth cell projection organization negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development cell projection morphogenesis neuron differentiation negative regulation of growth neuron projection morphogenesis cell differentiation regulation of biological quality system development regulation of biological process negative regulation of cellular component organization regulation of cell projection organization negative regulation of cell growth nervous system development developmental growth involved in morphogenesis generation of neurons negative regulation of axonogenesis negative regulation of developmental growth negative regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis regulation of axon extension cellular component organization regulation of nervous system development neurogenesis 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 cellular component organization or biogenesis negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth negative regulation of developmental process biological regulation growth negative regulation of axon extension axon development regulation of cell growth cell morphogenesis involved in neuron differentiation negative regulation of neuron projection development negative regulation of cell development neuron development cellular process regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size axon guidance anterior/posterior axon guidance neuron projection guidance establishment of organelle localization cellular localization transport nucleus localization intracellular transport establishment of localization localization organelle localization establishment of localization in cell nuclear migration apoptotic process cell death programmed cell death cellular response to stimulus negative chemotaxis response to stimulus taxis chemorepulsion of axon locomotion chemotaxis response to external stimulus cellular response to chemical stimulus response to chemical positive regulation of nervous system development positive regulation of developmental process positive regulation of cell projection organization positive regulation of developmental growth positive regulation of cell development positive regulation of multicellular organismal process positive regulation of cellular component organization positive regulation of biological process positive regulation of cell differentiation positive regulation of neurogenesis positive regulation of axon extension positive regulation of cellular process positive regulation of axonogenesis positive regulation of cell growth positive regulation of growth epithelium development tube development mammary gland morphogenesis mammary gland development gland development morphogenesis of an epithelium tissue development mammary gland duct morphogenesis tissue morphogenesis tube morphogenesis gland morphogenesis mammary gland epithelium development epithelial tube morphogenesis neuron migration motor neuron migration cell migration cell motility substrate-dependent cell migration, cell extension plasma membrane bounded cell projection assembly cellular component biogenesis cellular component assembly substrate-dependent cell migration cell projection assembly small GTPase-mediated signal transduction signaling Ras protein signal transduction intracellular signal transduction cell communication intracellular signaling cassette signal transduction regulation of cell motility glial cell migration regulation of glial cell migration gliogenesis regulation of locomotion regulation of cell migration Cdc42 protein signal transduction Rho protein signal transduction cell junction assembly regulation of synapse structure or activity regulation of synapse assembly synapse organization regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly 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 transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II 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 cell-cell adhesion positive regulation of locomotion positive regulation of cell motility positive regulation of cell population proliferation regulation of gliogenesis positive regulation of glial cell proliferation positive regulation of gliogenesis regulation of glial cell proliferation cell population proliferation regulation of cell population proliferation glial cell proliferation	basement membrane cell periphery extracellular matrix cellular anatomical structure external encapsulating structure intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm cytosol basement membrane cell periphery extracellular matrix cellular anatomical structure external encapsulating structure intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen synapse cell junction glutamatergic synapse extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, G [auth H], J [auth E]	IPR010560	Neogenin, C-terminal	Domain
B, G [auth H], J [auth E]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, G [auth H], J [auth E]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, G [auth H], J [auth E]	IPR003598	Immunoglobulin subtype 2	Domain
B, G [auth H], J [auth E]	IPR003961	Fibronectin type III	Domain
B, G [auth H], J [auth E]	IPR003599	Immunoglobulin domain subtype	Domain
B, G [auth H], J [auth E]	IPR007110	Immunoglobulin-like domain	Domain
B, G [auth H], J [auth E]	IPR013098	Immunoglobulin I-set	Domain
B, G [auth H], J [auth E]	IPR036116	Fibronectin type III superfamily	Homologous Superfamily
C [auth F], E [auth C], K [auth I]	IPR010536	Repulsive guidance molecule, N-terminal	Domain
C [auth F], E [auth C], K [auth I]	IPR009496	Repulsive guidance molecule, C-terminal	Domain
C [auth F], E [auth C], K [auth I]	IPR040287	Repulsive guidance molecule	Family
D [auth N], H [auth M], L [auth O]	IPR010536	Repulsive guidance molecule, N-terminal	Domain
D [auth N], H [auth M], L [auth O]	IPR009496	Repulsive guidance molecule, C-terminal	Domain
D [auth N], H [auth M], L [auth O]	IPR040287	Repulsive guidance molecule	Family
A, F [auth G], I [auth D]	IPR008211	Laminin, N-terminal	Domain
A, F [auth G], I [auth D]	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A, F [auth G], I [auth D]	IPR002049	Laminin-type EGF domain	Domain
A, F [auth G], I [auth D]	IPR018933	Netrin module, non-TIMP type	Domain
A, F [auth G], I [auth D]	IPR001134	Netrin domain	Domain
A, F [auth G], I [auth D]	IPR008993	Tissue inhibitor of metalloproteinases-like, OB-fold	Homologous Superfamily
A, F [auth G], I [auth D]	IPR056863	Laminin/attractin/netrin-like, EGF domain	Domain
A, F [auth G], I [auth D]	IPR050440	Laminin/Netrin Extracellular Matrix	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth F], E [auth C], K [auth I]	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
D [auth N], H [auth M], L [auth O]	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, F [auth G], I [auth D]	Pharos: O95631	astrocytic tumor brain edema Hashimoto thyroiditis medulloblastoma pancreatic ductal adenocarcinoma psoriasis atypical teratoid rhabdoid tumor cleft lip malignant ependymoma Neurobehavioral Manifestations pilocytic astrocytoma subarachnoid hemorrhage bone disease glioblastoma malignant glioma astrocytic tumor brain edema Hashimoto thyroiditis medulloblastoma pancreatic ductal adenocarcinoma psoriasis atypical teratoid rhabdoid tumor cleft lip malignant ependymoma Neurobehavioral Manifestations pilocytic astrocytoma subarachnoid hemorrhage bone disease glioblastoma malignant glioma oligodendroglioma primitive neuroectodermal tumor