- PDB-4kax: Crystal structure of the Grp1 PH domain in complex with Arf6-GTP -
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Basic information
Entry
Database: PDB / ID: 4kax
Title
Crystal structure of the Grp1 PH domain in complex with Arf6-GTP
Components
ADP-ribosylation factor 6
Cytohesin-3
Keywords
PROTEIN BINDING/SIGNALING PROTEIN / PH domain / Phosphoinositides / PROTEIN BINDING-SIGNALING PROTEIN complex
Function / homology
Function and homology information
erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / Intra-Golgi traffic / Golgi vesicle transport / regulation of dendritic spine development / establishment of epithelial cell polarity / protein localization to endosome / negative regulation of protein localization to cell surface ...erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / Intra-Golgi traffic / Golgi vesicle transport / regulation of dendritic spine development / establishment of epithelial cell polarity / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of dendrite development / negative regulation of receptor-mediated endocytosis / regulation of Rac protein signal transduction / ruffle assembly / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / regulation of ARF protein signal transduction / MET receptor recycling / thioesterase binding / endocytic recycling / filopodium membrane / Flemming body / protein localization to cell surface / TBC/RABGAPs / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / hepatocyte apoptotic process / phosphatidylinositol-3,4,5-trisphosphate binding / cleavage furrow / regulation of presynapse assembly / synaptic vesicle endocytosis / positive regulation of cell adhesion / endocytic vesicle / bicellular tight junction / signaling adaptor activity / vesicle-mediated transport / ruffle / guanyl-nucleotide exchange factor activity / small monomeric GTPase / cellular response to nerve growth factor stimulus / G protein activity / liver development / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / adherens junction / intracellular protein transport / positive regulation of neuron projection development / recycling endosome membrane / GDP binding / presynapse / Clathrin-mediated endocytosis / nervous system development / cell cortex / early endosome membrane / midbody / postsynapse / cell differentiation / cell adhesion / endosome / cell cycle / cell division / Golgi membrane / focal adhesion / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function
ADP-ribosylation factor 6 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type ...ADP-ribosylation factor 6 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology
Mass: 19530.291 Da / Num. of mol.: 1 / Fragment: Arf6 (residues 14-181) / Mutation: Q67L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARF6 / Production host: Escherichia coli (E. coli) / References: UniProt: P62330
#2: Protein
Cytohesin-3 / ARF nucleotide-binding site opener 3 / Protein ARNO3 / General receptor of phosphoinositides 1 / ...ARF nucleotide-binding site opener 3 / Protein ARNO3 / General receptor of phosphoinositides 1 / Grp1 / PH / SEC7 and coiled-coil domain-containing protein 3
Mass: 19038.633 Da / Num. of mol.: 1 / Fragment: Grp1 PH domain (residues 247-399) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYTH3, ARNO3, GRP1, PSCD3 / Production host: Escherichia coli (E. coli) / References: UniProt: O43739
Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal grow
Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 50 mM Tris, 20% PEG 4000, 0.2 M sodium citrate. Microseeding and TCEP were needed for large crystal growth, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
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