4URT | pdb_00004urt

The crystal structure of a fragment of netrin-1 in complex with FN5- FN6 of DCC

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	fn3	e4urtB2	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	Laminin_N	e4urtA1	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	e4urtA2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF_1	ECOD (1.6)
A	Laminin_EGF	e4urtA4	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF	ECOD (1.6)
A	Laminin_EGF_2	e4urtA3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.2.0)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00041	Fibronectin type III domain (fn3)	Fibronectin type III domain		Domain
A	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	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	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	NETRIN RECEPTOR DCC	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	multicellular organismal process regulation of growth regulation of cellular process axonogenesis regulation of cellular component size cell projection organization developmental growth negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development multicellular organism development cell projection morphogenesis neuron differentiation multicellular organismal process regulation of growth regulation of cellular process axonogenesis regulation of cellular component size cell projection organization developmental growth negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development multicellular organism development cell projection morphogenesis neuron differentiation negative regulation of growth neuron projection morphogenesis cell differentiation anatomical structure development regulation of biological quality system development developmental process 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 collateral sprouting regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis 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 regulation of multicellular organismal development collateral sprouting regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth negative regulation of developmental process biological regulation growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation negative regulation of neuron projection development anatomical structure morphogenesis negative regulation of cell development neuron development cellular process negative regulation of collateral sprouting regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size axon guidance dorsal/ventral axon guidance neuron projection guidance anterior/posterior axon guidance apoptotic process cell death programmed cell death dendrite development negative regulation of dendrite development regulation of dendrite development trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission signaling cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling postsynaptic modulation of chemical synaptic transmission regulation of cell communication central nervous system neuron development central nervous system neuron differentiation spinal cord development spinal cord ventral commissure morphogenesis central nervous system projection neuron axonogenesis central nervous system neuron axonogenesis central nervous system development neuron migration cell migration cell motility cell adhesion cell-cell adhesion	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 intracellular anatomical structure cytoplasm cytosol Schaffer collateral - CA1 synapse axon cell projection neuron projection plasma membrane bounded cell projection
A	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	IPR010560	Neogenin, C-terminal	Domain
B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B	IPR003598	Immunoglobulin subtype 2	Domain
B	IPR003599	Immunoglobulin domain subtype	Domain
B	IPR013098	Immunoglobulin I-set	Domain
B	IPR003961	Fibronectin type III	Domain
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR007110	Immunoglobulin-like domain	Domain
B	IPR036116	Fibronectin type III superfamily	Homologous Superfamily
A	IPR008211	Laminin, N-terminal	Domain
A	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A	IPR002049	Laminin-type EGF domain	Domain
A	IPR018933	Netrin module, non-TIMP type	Domain
A	IPR001134	Netrin domain	Domain
A	IPR008993	Tissue inhibitor of metalloproteinases-like, OB-fold	Homologous Superfamily
A	IPR056863	Laminin/attractin/netrin-like, EGF domain	Domain
A	IPR050440	Laminin/Netrin Extracellular Matrix	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P43146	mirror movements 1 colorectal cancer melanoma intellectual disability esophageal cancer gaze palsy, familial horizontal, with progressive scoliosis, 2 corpus callosum, agenesis of horizontal gaze palsy with progressive scoliosis familial congenital mirror movements gastroesophageal reflux disease lung adenocarcinoma Agenesis of corpus callosum medulloblastoma benign neoplasm of esophagus carcinoma of esophagus mirror movements 1 colorectal cancer melanoma intellectual disability esophageal cancer gaze palsy, familial horizontal, with progressive scoliosis, 2 corpus callosum, agenesis of horizontal gaze palsy with progressive scoliosis familial congenital mirror movements gastroesophageal reflux disease lung adenocarcinoma Agenesis of corpus callosum medulloblastoma benign neoplasm of esophagus carcinoma of esophagus neoplasm of esophagus pituitary cancer schizophrenia Ehlers-Danlos syndrome gallbladder cancer Kallmann syndrome lung carcinoma attention deficit hyperactivity disorder, inattentive type bipolar disorder non-small cell lung carcinoma colorectal carcinoma endogenous depression esophagus carcinoma in situ gallbladder carcinoma large cell medulloblastoma malignant ependymoma autism spectrum disorder cancer pilocytic astrocytoma colorectal adenocarcinoma psoriasis cutaneous melanoma eosinophilic esophagitis
A	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

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.