3BRW | pdb_00003brw

Structure of the Rap-RapGAP 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)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Rap/Ran-GAP	8039746	3001969	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Rap/Ran-GAP	8039746	3001969	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Rap/Ran-GAP	8039746	3001969	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)
D	SCP2	e3brwD1	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: SCP2	ECOD (v294.1)
C	Me-amine-dh_H	e3brwC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Me-amine-dh_H	ECOD (v294.1)
B	PSI_PsaE	e3brwB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Helical bundle in flu nucleocapsid protein	T: Helical bundle in flu nucleocapsid protein	F: PSI_PsaE	ECOD (v294.1)
A	Rieske_2	e3brwA3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: Rieske_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.30.1120.160	Alpha Beta	2-Layer Sandwich	Arylsulfatase, C-terminal domain		CATH (4.3.0)
C	3.40.50.11210	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Rap/Ran-GAP	CATH (4.3.0)
B	3.30.1120.160	Alpha Beta	2-Layer Sandwich	Arylsulfatase, C-terminal domain		CATH (4.3.0)
B	3.40.50.11210	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Rap/Ran-GAP	CATH (4.3.0)
A	3.30.1120.160	Alpha Beta	2-Layer Sandwich	Arylsulfatase, C-terminal domain		CATH (4.3.0)
A	3.40.50.11210	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Rap/Ran-GAP	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	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	PF21022	Rap/Ran-GAP protein dimerization domain (Rap-GAP_dimer)	Rap/Ran-GAP protein dimerization domain	This entry represents an alpha+beta domain found in some Rap-GAP proteins. It mediates dimerization in Rap1GAP protein [1].	Domain
A, B, C	PF02145	Rap/ran-GAP (Rap_GAP)	Rap/ran-GAP		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	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 vesicle extracellular membrane-bounded organelle intracellular anatomical structure cellular anatomical structure membrane cell-cell junction anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle 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	Rap1 GTPase-activating protein 1	small GTPase binding protein binding binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity identical protein binding protein homodimerization activity small GTPase binding protein binding binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity identical protein binding protein homodimerization activity protein dimerization activity 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	multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation response to stimulus immune response immune system process adaptive immune response localization import into cell transport phagocytosis endocytosis establishment of localization vesicle-mediated transport positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity positive regulation of cell adhesion regulation of cell adhesion positive regulation of biological process positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion regulation of cell-cell adhesion positive regulation of cellular process regulation of localization positive regulation of cellular component organization regulation of cellular component organization cellular component organization positive regulation of endocytosis cellular component organization or biogenesis regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of phagocytosis positive regulation of transport thyroid gland development negative regulation of thyroid gland epithelial cell proliferation gland development thyroid gland epithelial cell proliferation regulation of multicellular organismal process epithelial cell proliferation negative regulation of cell population proliferation cell population proliferation endocrine system development animal organ development regulation of cell population proliferation regulation of thyroid gland epithelial cell proliferation regulation of epithelial cell proliferation negative regulation of multicellular organismal process negative regulation of epithelial cell proliferation response to glial cell derived neurotrophic factor cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to glial cell derived neurotrophic factor response to growth factor cell projection organization plasma membrane bounded cell projection assembly microvillus organization cellular component biogenesis regulation of microvillus assembly negative regulation of plasma membrane bounded cell projection assembly cellular component assembly negative regulation of cell projection organization plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of microvillus organization regulation of plasma membrane bounded cell projection assembly negative regulation of microvillus assembly microvillus assembly cell projection assembly regulation of plasma membrane bounded cell projection organization cellular response to stimulus signaling signal transduction cell communication cellular localization establishment of localization in cell regulation of signaling small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette regulation of cell communication	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle early endosome endosome cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle vesicle Golgi membrane Golgi apparatus bounding membrane of organelle organelle membrane cell body neuronal cell body axon

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D	IPR005225	Small GTP-binding domain	Domain
D	IPR020849	Small GTPase, Ras-type	Family
D	IPR001806	Small GTPase	Family
D	IPR038851	Ras-related protein Rap1	Family
A, B, C	IPR003109	GoLoco motif	Conserved Site
A, B, C	IPR000331	Rap/Ran-GAP domain	Domain
A, B, C	IPR035974	Rap/Ran-GAP superfamily	Homologous Superfamily
A, B, C	IPR050989	Rap1/Ran GTPase-activating	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D	Pharos: P61224	Kabuki syndrome lung adenocarcinoma
A, B, C	Pharos: P47736	melanoma acute promyelocytic leukemia thyroid adenoma malignant pancreatic neoplasm thyroid gland carcinoma ovarian cancer Pick disease Thyroid Neoplasm astrocytic tumor glioblastoma large cell medulloblastoma malignant glioma nephrolithiasis pancreatic ductal adenocarcinoma pilocytic astrocytoma melanoma acute promyelocytic leukemia thyroid adenoma malignant pancreatic neoplasm thyroid gland carcinoma ovarian cancer Pick disease Thyroid Neoplasm astrocytic tumor glioblastoma large cell medulloblastoma malignant glioma nephrolithiasis pancreatic ductal adenocarcinoma pilocytic astrocytoma thyroid cancer adrenal cortex carcinoma atypical teratoid rhabdoid tumor interstitial cystitis lung cancer medulloblastoma oligodendroglioma pancreatic neoplasm primitive neuroectodermal tumor aortic stenosis cutaneous melanoma ductal breast carcinoma in situ invasive ductal breast carcinoma malignant ependymoma

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.