5V6R | pdb_00005v6r

Structure of Plexin D1 intracellular domain

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e5v6rB1	A: Repetitive alpha hairpins	X: Nucleotidyltransferase	H: Nucleotidyltransferase	T: Plexin_RBD	F:	ECOD (20:10:01)
A		e5v6rA1	A: Repetitive alpha hairpins	X: Nucleotidyltransferase	H: Nucleotidyltransferase	T: Plexin_RBD	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.506.10	Mainly Alpha	Orthogonal Bundle	GTPase Activation - p120GAP	domain 1	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A	1.10.506.10	Mainly Alpha	Orthogonal Bundle	GTPase Activation - p120GAP	domain 1	CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF20170	Plexin cytoplasmic RhoGTPase-binding domain (Plexin_RBD)	Plexin cytoplasmic RhoGTPase-binding domain	This entry represents the RhoGTPase-binding domain found in the cytoplasmic domain of plexins [1].	Domain
A, B	PF08337	Plexin cytoplasmic RasGAP domain (Plexin_cytopl)	Plexin cytoplasmic RasGAP domain	This family features the C-terminal regions of various plexins (e.g. Swiss:P51805). Plexins are receptors for semaphorins, and plexin signalling is important in path finding and patterning of both neurons and developing blood vessels [1,2]. The cytop ...	This family features the C-terminal regions of various plexins (e.g. Swiss:P51805). Plexins are receptors for semaphorins, and plexin signalling is important in path finding and patterning of both neurons and developing blood vessels [1,2]. The cytoplasmic region, which has been called a SEX domain in some members of this family [3], is involved in downstream signalling pathways, by interaction with proteins such as Rac1, RhoD, Rnd1 and other plexins [4]. This domain acts as a RasGAP domain [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Plexin-D1	protein binding binding protein domain specific binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity semaphorin receptor activity	developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development heart development cardiac septum development cardiac chamber development animal organ development endothelial cell migration cell migration cellular process cell motility positive regulation of nervous system development axonogenesis regulation of cellular process cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation positive regulation of cell projection organization regulation of cell projection organization positive regulation of cell development nervous system development generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cellular developmental process plasma membrane bounded cell projection morphogenesis positive regulation of biological process cell development cell morphogenesis cellular component organization regulation of nervous system development neurogenesis positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis cellular component organization or biogenesis positive regulation of axonogenesis positive regulation of cellular process plasma membrane bounded cell projection organization axon development cell morphogenesis involved in neuron differentiation neuron development regulation of plasma membrane bounded cell projection organization artery development aorta 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 regulation of cell motility regulation of locomotion regulation of cell migration locomotion regulation of cell shape regulation of cell morphogenesis regulation of biological quality branching morphogenesis of an epithelial tube epithelial tube morphogenesis epithelium development morphogenesis of an epithelium tissue development branching involved in blood vessel morphogenesis tissue morphogenesis morphogenesis of a branching structure morphogenesis of a branching epithelium cellular response to stimulus cell surface receptor signaling pathway response to stimulus semaphorin-plexin signaling pathway signaling cell communication signal transduction gland development branching involved in salivary gland morphogenesis salivary gland development dichotomous subdivision of terminal units involved in salivary gland branching gland morphogenesis dichotomous subdivision of an epithelial terminal unit salivary gland morphogenesis animal organ morphogenesis exocrine system development neuron recognition synaptic target recognition cell recognition coronary vasculature development cellular component biogenesis cell junction organization cellular component assembly cell junction assembly synapse organization synapse assembly kidney development renal system development cell adhesion regulation of cell adhesion negative regulation of cell adhesion heart morphogenesis outflow tract morphogenesis	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium cell periphery plasma membrane membrane protein-containing complex semaphorin receptor complex receptor complex synapse cell junction glutamatergic synapse cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium cell periphery plasma membrane membrane protein-containing complex semaphorin receptor complex receptor complex synapse cell junction glutamatergic synapse leading edge membrane plasma membrane region lamellipodium membrane cell projection membrane axon neuron projection cell body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002909	IPT domain	Domain
A, B	IPR016201	PSI domain	Domain
A, B	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B	IPR008936	Rho GTPase activation protein	Homologous Superfamily
A, B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B	IPR002165	Plexin repeat	Repeat
A, B	IPR041019	Plexin, TIG domain 1	Domain
A, B	IPR031148	Plexin family	Family
A, B	IPR046800	Plexin, cytoplasmic RhoGTPase-binding domain	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR042719	Plexin-D1, sema domain	Domain
A, B	IPR013548	Plexin, cytoplasmic RasGAP domain	Domain
A, B	IPR036352	Sema domain superfamily	Homologous Superfamily
A, B	IPR001627	Sema domain	Domain

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.