7NDG

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)
E [auth C]	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)
C [auth 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	PF00055	e7ndgA3	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: PF00055	ECOD (1.6)
A	PF00053	e7ndgA2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: PF00053	ECOD (1.6)
I [auth D]	PF00055	e7ndgD3	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: PF00055	ECOD (1.6)
I [auth D]	PF00053	e7ndgD4	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: PF00053	ECOD (1.6)
F [auth G]	PF00055	e7ndgG1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: PF00055	ECOD (1.6)
F [auth G]	PF00053	e7ndgG4	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: PF00053	ECOD (1.6)
B	PF00041	e7ndgB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00041	ECOD (1.6)
G [auth H]	PF00041	e7ndgH3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00041	ECOD (1.6)
J [auth E]	PF00041	e7ndgE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00041	ECOD (1.6)
E [auth C]	PF06534,PF06535	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: PF06534,PF06535	ECOD (1.6)
K [auth I]	PF06534,PF06535	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: PF06534,PF06535	ECOD (1.6)
C [auth F]	PF06534,PF06535	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: PF06534,PF06535	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, F [auth G], I [auth D]	PF00053	Laminin EGF domain (Laminin_EGF)	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
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]	PF06535	Repulsive guidance molecule (RGM) N-terminus (RGM_N)	Repulsive guidance molecule (RGM) N-terminus	-	Family
C [auth F], E [auth C], K [auth I]	PF06534	Repulsive guidance molecule (RGM) C-terminus (RGM_C)	Repulsive guidance molecule (RGM) C-terminus	-	Family
D [auth N], H [auth M], L [auth O]	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, 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 organic cyclic compound 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 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 organic cyclic compound 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 cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process cellular metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription 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 external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle cytoplasm basement membrane cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen extracellular region
B, G [auth H], J [auth E]	Neogenin	-	-	membrane cellular anatomical entity
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 macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process primary metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic 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 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 macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process primary metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic 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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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]	IPR003599	Immunoglobulin subtype	Domain
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]	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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
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
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