4KVG | pdb_00004kvg

Crystal structure of RIAM RA-PH domains in complex with GTP bound Rap1

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)
C	d4kvgc_	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)
A	d4kvga1	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)
A	d4kvga2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8057410	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8057410	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)
D		e4kvgD3	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T:	F:	ECOD (20:10:01)
B		e4kvgB1	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: Rep-A_N	F:	ECOD (20:10:01)
C		e4kvgC1	A: DEATH domain	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: Rep-A_N	F:	ECOD (20:10:01)
A		e4kvgA1	A: jelly-roll	X: Double-stranded beta-helix	H: Double-stranded beta-helix	T: Bromodomain	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	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)
B	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	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
B, D	PF00788	Ras association (RalGDS/AF-6) domain (RA)	Ras association (RalGDS/AF-6) domain	RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Recent evidence (not yet in MEDLINE) shows that some RA domains do NOT bind RasGTP. Predicted structure [3] similar to that determined [1], and that of th ...	RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Recent evidence (not yet in MEDLINE) shows that some RA domains do NOT bind RasGTP. Predicted structure [3] similar to that determined [1], and that of the RasGTP-binding domain of Raf kinase.	Domain
B, D	PF00169	PH domain (PH)	PH domain	PH stands for pleckstrin homology.	Domain
A, C	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Amyloid beta A4 precursor protein-binding family B member 1-interacting protein	-	regulation of biological process cell adhesion regulation of cellular process positive regulation of cell adhesion regulation of cell adhesion biological regulation positive regulation of biological process cellular process positive regulation of cellular process multicellular organismal process response to stimulus immune response cell activation lymphocyte activation regulation of biological process cell adhesion regulation of cellular process positive regulation of cell adhesion regulation of cell adhesion biological regulation positive regulation of biological process cellular process positive regulation of cellular process multicellular organismal process response to stimulus immune response cell activation lymphocyte activation cell activation involved in immune response leukocyte activation immune effector process T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell T cell activation involved in immune response T cell activation immune system process leukocyte activation involved in immune response lymphocyte activation involved in immune response cellular response to stimulus signaling signal transduction cell communication	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell projection cell leading edge plasma membrane bounded cell projection lamellipodium cell periphery protein-containing complex plasma membrane protein complex membrane plasma membrane cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell projection cell leading edge plasma membrane bounded cell projection lamellipodium cell periphery protein-containing complex plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex T cell receptor complex receptor complex intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle cytoplasm cytosol
A, C	Ras-related protein Rap-1A	small GTPase binding protein binding binding enzyme binding GTPase binding protein-containing complex 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 guanyl nucleotide binding small GTPase binding protein binding binding enzyme binding GTPase binding protein-containing complex 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 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 GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity G protein activity	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 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 process cellular response to stimulus small GTPase-mediated signal transduction response to stimulus intracellular signal transduction intracellular signaling cassette signal transduction Rap protein signal transduction regulation of biosynthetic process negative regulation of collagen metabolic process negative regulation of metabolic process collagen biosynthetic process regulation of collagen biosynthetic process regulation of collagen metabolic process negative regulation of collagen biosynthetic process biosynthetic process negative regulation of biosynthetic process metabolic process collagen metabolic process regulation of metabolic process multicellular organismal process regulation of developmental process cellular developmental process positive regulation of biological process regulation of vasculogenesis regulation of cell differentiation vasculogenesis positive regulation of developmental process multicellular organism development tube morphogenesis positive regulation of cell differentiation cell differentiation anatomical structure development positive regulation of cellular process blood vessel development system development developmental process blood vessel morphogenesis tube development vasculature development circulatory system development anatomical structure morphogenesis positive regulation of vasculogenesis protein localization to cell periphery protein localization to plasma membrane macromolecule localization intracellular protein localization localization within membrane protein localization to membrane import into cell positive regulation of cellular component organization regulation of cellular component organization cellular component organization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis regulation of endocytosis regulation of phagocytosis positive regulation of phagocytosis positive regulation of transport endocytosis cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus response to nerve growth factor response to growth factor regulation of neuron projection development cell projection organization cell development neuron projection development neurogenesis neuron differentiation positive regulation of neuron projection development positive regulation of cell projection organization plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization regulation of cellular component biogenesis regulation of cell junction assembly cellular component biogenesis cell junction organization cellular component assembly cell junction assembly regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of molecular function positive regulation of protein modification process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein kinase activity phosphorus metabolic process protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process positive regulation of catalytic activity primary metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process positive regulation of cell communication immune response-regulating cell surface receptor signaling pathway positive regulation of signal transduction regulation of signal transduction positive regulation of response to stimulus regulation of Fc receptor mediated stimulatory signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process cell surface receptor signaling pathway immune response immune response-activating cell surface receptor signaling pathway Fc receptor mediated stimulatory signaling pathway positive regulation of Fc receptor mediated stimulatory signaling pathway regulation of response to stimulus immune system process regulation of immune response activation of immune response positive regulation of signaling nerve growth factor signaling pathway neurotrophin signaling pathway positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of hydrolase activity regulation of hydrolase activity regulation of GTPase activity positive regulation of GTPase activity gland development animal organ development animal organ regeneration liver development regeneration hepaticobiliary system development liver regeneration 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 protein localization to synapse regulation of protein localization regulation of neurotransmitter receptor localization to postsynaptic specialization membrane regulation of protein localization to synapse neurotransmitter receptor localization to postsynaptic specialization membrane regulation of biological quality regulation of protein localization to membrane regulation of receptor localization to synapse protein localization to postsynaptic specialization membrane protein localization to postsynaptic membrane regulation of protein localization to cell periphery protein-containing complex localization regulation of postsynaptic membrane neurotransmitter receptor levels regulation of cellular localization protein localization to organelle protein localization to postsynapse protein localization to cell junction receptor localization to synapse response to antineoplastic agent epithelium development endothelial cell differentiation endothelium development tissue development epithelial cell differentiation endothelial cell development epithelial cell development establishment of endothelial barrier hexose transmembrane transport regulation of D-glucose import across plasma membrane carbohydrate import across plasma membrane carbohydrate transport positive regulation of D-glucose transmembrane transport hexose import across plasma membrane positive regulation of transmembrane transport positive regulation of D-glucose import across plasma membrane import across plasma membrane transmembrane transport regulation of transmembrane transport D-glucose import across plasma membrane D-glucose transmembrane transport regulation of D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport response to carbohydrate response to ketone response to lipid response to alcohol cellular response to forskolin cellular response to alcohol response to forskolin cellular response to lipid cellular response to ketone	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane specific granule extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol cell projection sperm midpiece cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection synapse cell junction glutamatergic synapse neuron projection perinuclear region of cytoplasm endosome membrane endosome phagocytic vesicle endocytic vesicle anchoring junction cell periphery plasma membrane presynapse protein-containing complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex early endosome late endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR001849	Pleckstrin homology domain	Domain
B, D	IPR000159	Ras-associating domain	Domain
B, D	IPR039664	GRB/APBB1IP	Family
B, D	IPR039665	APBB1IP, PH domain	Domain
B, D	IPR011993	PH-like domain superfamily	Homologous Superfamily
B, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C	IPR020849	Small GTPase, Ras-type	Family
A, C	IPR038851	Ras-related protein Rap1	Family
A, C	IPR005225	Small GTP-binding domain	Domain
A, C	IPR001806	Small GTPase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P62834	Kabuki syndrome atypical teratoid rhabdoid tumor cystic fibrosis invasive ductal breast carcinoma lung adenocarcinoma non-small cell lung carcinoma breast cancer glioblastoma malignant ependymoma oligodendroglioma Crohn disease hereditary spastic paraplegia large cell medulloblastoma malignant glioma psoriasis

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.