3Q3J

Crystal structure of plexin A2 RBD in complex with Rnd1

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3q3ja_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3q3jb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057508	3002022	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	Plexin_cytopl_2nd	e3q3jA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Plexin_cytopl_2nd	ECOD (1.6)
B	Ras	e3q3jB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
B	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motil ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Plexin-A2	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity semaphorin receptor activity identical protein binding protein binding binding	developmental process multicellular organismal process limb development appendage development limb bud formation anatomical structure morphogenesis multicellular organism development appendage morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development limb morphogenesis localization centrosome localization microtubule organizing center localization developmental process multicellular organismal process limb development appendage development limb bud formation anatomical structure morphogenesis multicellular organism development appendage morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development limb morphogenesis localization centrosome localization microtubule organizing center localization cellular process somitogenesis epithelium development chordate embryonic development segmentation anterior/posterior pattern specification pattern specification process embryo development tissue development regionalization embryo development ending in birth or egg hatching somite development 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 system development regulation of biological process 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 regulation of 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 regulation of multicellular organismal process cellular component organization or biogenesis positive regulation of axonogenesis regulation of anatomical structure morphogenesis positive regulation of cellular process regulation of multicellular organismal development plasma membrane bounded cell projection organization biological regulation axon development cell morphogenesis involved in neuron differentiation neuron development regulation of plasma membrane bounded cell projection organization regulation of cell motility regulation of locomotion regulation of cell migration cell migration cell motility locomotion head development animal organ development brain development central nervous system development cerebellar granule cell precursor tangential migration hindbrain development hindbrain tangential cell migration cell migration in hindbrain pharyngeal system development regulation of cell shape regulation of cell morphogenesis regulation of biological quality cellular response to stimulus cell surface receptor signaling pathway response to stimulus semaphorin-plexin signaling pathway signaling cell communication signal transduction neural tube development tube development cell adhesion regulation of cell adhesion negative regulation of cellular process negative regulation of biological process negative regulation of cell adhesion	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex semaphorin receptor complex receptor complex
B	Rho-related GTP-binding protein Rho6	protein binding binding signaling receptor binding kinase binding enzyme binding protein kinase binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding protein binding binding signaling receptor binding kinase binding enzyme binding protein kinase binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	developmental process multicellular organismal process cellular developmental process cell development developmental maturation nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation neuron remodeling anatomical structure maturation cell differentiation neuron development anatomical structure development developmental process multicellular organismal process cellular developmental process cell development developmental maturation nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation neuron remodeling anatomical structure maturation cell differentiation neuron development anatomical structure development neuron maturation cellular process cell maturation system development regulation of cytoskeleton organization regulation of biological process regulation of cellular component organization regulation of cellular process regulation of actin filament-based process actin cytoskeleton organization biological regulation regulation of organelle organization cellular component organization organelle organization regulation of actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization actin filament organization supramolecular fiber organization cell migration cell motility cellular response to stimulus response to stimulus signaling signal transduction cell communication small GTPase-mediated signal transduction intracellular signal transduction intracellular signaling cassette cell adhesion regulation of cell adhesion negative regulation of cellular process negative regulation of biological process negative regulation of cell adhesion	cell-cell junction adherens junction anchoring junction cell junction cellular anatomical entity intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle cytoplasm cytosol cell-cell junction adherens junction anchoring junction cell junction cellular anatomical entity intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002909	IPT domain	Domain
A	IPR042826	Plexin-A2, sema domain	Domain
A	IPR041362	Plexin, TIG domain 2	Domain
A	IPR016201	PSI domain	Domain
A	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A	IPR008936	Rho GTPase activation protein	Homologous Superfamily
A	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A	IPR002165	Plexin repeat	Repeat
A	IPR041019	Plexin, TIG domain 1	Domain
A	IPR031148	Plexin family	Family
A	IPR046800	Plexin, cytoplasmic RhoGTPase-binding domain	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR013548	Plexin, cytoplasmic RasGAP domain	Domain
A	IPR036352	Sema domain superfamily	Homologous Superfamily
A	IPR001627	Sema domain	Domain
B	IPR005225	Small GTP-binding domain	Domain
B	IPR001806	Small GTPase	Family
B	IPR003578	Small GTPase Rho	Family
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O75051	schizophrenia atypical teratoid rhabdoid tumor idiopathic scoliosis malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma breast cancer large cell medulloblastoma medulloblastoma osteosarcoma pilocytic astrocytoma glioblastoma malignant glioma mixed anxiety and depressive disorder ovarian cancer
B	Pharos: Q92730	astrocytic tumor large cell medulloblastoma malignant glioma oligodendroglioma psoriasis atypical teratoid rhabdoid tumor lung cancer medulloblastoma pilocytic astrocytoma glioblastoma malignant ependymoma non-small cell lung carcinoma 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.