4M8N | pdb_00004m8n

Crystal Structure of PlexinC1/Rap1B Complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	3002022	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	3002022	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	3002022	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	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)
F	Ras	e4m8nF1	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)
H	Ras	e4m8nH1	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)
G	Ras	e4m8nG1	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)
E	Ras	e4m8nE1	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)
D	Plexin_cytopl_1st	e4m8nD3	A: alpha bundles	X: GTPase activation domain, GAP (From Topology)	H: GTPase activation domain, GAP (From Topology)	T: GTPase activation domain, GAP	F: Plexin_cytopl_1st	ECOD (1.6)
D	Plexin_cytopl_2nd	e4m8nD4	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Plexin_cytopl_2nd	ECOD (1.6)
C	Plexin_cytopl_1st	e4m8nC1	A: alpha bundles	X: GTPase activation domain, GAP (From Topology)	H: GTPase activation domain, GAP (From Topology)	T: GTPase activation domain, GAP	F: Plexin_cytopl_1st	ECOD (1.6)
C	Plexin_cytopl_2nd	e4m8nC2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Plexin_cytopl_2nd	ECOD (1.6)
B	Plexin_cytopl_1st	e4m8nB1	A: alpha bundles	X: GTPase activation domain, GAP (From Topology)	H: GTPase activation domain, GAP (From Topology)	T: GTPase activation domain, GAP	F: Plexin_cytopl_1st	ECOD (1.6)
B	Plexin_cytopl_2nd	e4m8nB2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Plexin_cytopl_2nd	ECOD (1.6)
A	Plexin_cytopl_1st	e4m8nA1	A: alpha bundles	X: GTPase activation domain, GAP (From Topology)	H: GTPase activation domain, GAP (From Topology)	T: GTPase activation domain, GAP	F: Plexin_cytopl_1st	ECOD (1.6)
A	Plexin_cytopl_2nd	e4m8nA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Plexin_cytopl_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
H	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
G	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	1.10.506.10	Mainly Alpha	Orthogonal Bundle	GTPase Activation - p120GAP	domain 1	CATH (4.3.0)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	1.10.506.10	Mainly Alpha	Orthogonal Bundle	GTPase Activation - p120GAP	domain 1	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
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
E, F, G, H	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, motili ...	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
A, B, C, D	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, C, D	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
E, F, G, H	Ras-related protein Rap-1b	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding GDP binding protein-containing complex binding pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	cellular component organization cell junction organization cellular process synapse organization cellular component organization or biogenesis modification of postsynaptic structure modification of synaptic structure regulation of localization regulated exocytosis regulation of cellular process synaptic vesicle cycle negative regulation of biological process synaptic vesicle exocytosis negative regulation of transport cellular component organization cell junction organization cellular process synapse organization cellular component organization or biogenesis modification of postsynaptic structure modification of synaptic structure regulation of localization regulated exocytosis regulation of cellular process synaptic vesicle cycle negative regulation of biological process synaptic vesicle exocytosis negative regulation of transport vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization negative regulation of secretion establishment of localization in cell negative regulation of secretion by cell trans-synaptic signaling regulation of biological process neurotransmitter secretion regulation of synaptic vesicle exocytosis neurotransmitter transport establishment of localization negative regulation of synaptic vesicle exocytosis regulation of secretion signal release from synapse regulation of trans-synaptic signaling exocytosis cellular localization transport modulation of chemical synaptic transmission signaling negative regulation of regulated secretory pathway regulation of regulated secretory pathway synaptic signaling regulation of secretion by cell secretion by cell negative regulation of exocytosis signal release negative regulation of cellular process regulation of signaling regulation of transport secretion regulation of neurotransmitter transport biological regulation export from cell cell-cell signaling regulation of vesicle-mediated transport chemical synaptic transmission regulation of neurotransmitter secretion anterograde trans-synaptic signaling regulation of exocytosis regulation of cell communication cellular response to stimulus small GTPase-mediated signal transduction response to stimulus intracellular signal transduction intracellular signaling cassette signal transduction Rap protein signal transduction calcium-ion regulated exocytosis positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction positive regulation of cellular process positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling cell population proliferation cellular response to nitrogen compound response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to cAMP regulation of calcium ion-dependent exocytosis negative regulation of calcium ion-dependent exocytosis positive regulation of cellular component organization regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly regulation of integrin activation integrin activation positive regulation of integrin activation regulation of cell junction assembly cell junction assembly developmental process epithelium development endothelial cell differentiation cellular developmental process endothelium development cell development tissue development epithelial cell differentiation endothelial cell development epithelial cell development cell differentiation establishment of endothelial barrier anatomical structure development regulation of establishment of cell polarity regulation of establishment or maintenance of cell polarity establishment of cell polarity establishment or maintenance of cell polarity	cellular anatomical structure membrane cell-cell junction anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cellular anatomical structure membrane cell-cell junction anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle lytic vacuole endomembrane system intracellular organelle bounding membrane of organelle vesicle membrane cytoplasmic vesicle lysosome vacuolar membrane azurophil granule vacuole intracellular membrane-bounded organelle lytic vacuole membrane cytoplasmic vesicle membrane lysosomal membrane secretory granule primary lysosome secretory vesicle azurophil granule membrane cytoplasm organelle membrane secretory granule membrane cytosol cell periphery plasma membrane synapse glutamatergic synapse lipid droplet membraneless organelle intracellular membraneless organelle
A, B, C, D	PlexinC1 Intracellular Region	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity semaphorin receptor activity	developmental process multicellular organism development multicellular organismal process anatomical structure development nervous system development system development	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
E, F, G, H	IPR005225	Small GTP-binding domain	Domain
E, F, G, H	IPR020849	Small GTPase, Ras-type	Family
E, F, G, H	IPR001806	Small GTPase	Family
E, F, G, H	IPR038851	Ras-related protein Rap1	Family
A, B, C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR002909	IPT domain	Domain
A, B, C, D	IPR008936	Rho GTPase activation protein	Homologous Superfamily
A, B, C, D	IPR013548	Plexin, cytoplasmic RasGAP domain	Domain
A, B, C, D	IPR036352	Sema domain superfamily	Homologous Superfamily
A, B, C, D	IPR001627	Sema domain	Domain
A, B, C, D	IPR031148	Plexin family	Family
A, B, C, D	IPR046800	Plexin, cytoplasmic RhoGTPase-binding domain	Domain
A, B, C, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F, G, H	Pharos: P61224	Kabuki syndrome lung adenocarcinoma

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.