[English] 日本語
Yorodumi- PDB-2w83: Crystal structure of the ARF6 GTPase in complex with a specific e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w83 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4 | ||||||
Components |
| ||||||
Keywords | PROTEIN TRANSPORT / GOLGI APPARATUS / ER-GOLGI TRANSPORT / ARF / GTPASE / EFFECTOR / MYRISTATE / CYTOPLASM / NUCLEOTIDE-BINDING / ALTERNATIVE SPLICING / GTP-BINDING / PHOSPHOPROTEIN / HETEROTETRAMER / TRANSPORT / COILED-COIL / LIPOPROTEIN / COILED COIL | ||||||
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 / 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 ...: / erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / 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 / MAP-kinase scaffold activity / lysosome localization / JUN kinase binding / MET receptor recycling / thioesterase binding / endocytic recycling / filopodium membrane / retrograde transport, endosome to Golgi / Flemming body / protein localization to cell surface / TBC/RABGAPs / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / positive regulation of muscle cell differentiation / Myogenesis / hepatocyte apoptotic process / kinesin binding / cleavage furrow / regulation of presynapse assembly / synaptic vesicle endocytosis / centriolar satellite / endocytic vesicle / signaling adaptor activity / vesicle-mediated transport / ruffle / striated muscle cell differentiation / positive regulation of neuron differentiation / small monomeric GTPase / cellular response to nerve growth factor stimulus / acrosomal vesicle / G protein activity / liver development / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / intracellular protein transport / positive regulation of neuron projection development / recycling endosome membrane / GDP binding / signaling receptor complex adaptor activity / presynapse / Clathrin-mediated endocytosis / nervous system development / cell cortex / early endosome membrane / midbody / postsynapse / cell differentiation / cell adhesion / endosome / positive regulation of cell migration / cell cycle / cell division / lysosomal membrane / focal adhesion / GTPase activity / glutamatergic synapse / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Isabet, T. / Montagnac, G. / Regazzoni, K. / Raynal, B. / El Khadali, F. / Franco, M. / England, P. / Chavrier, P. / Houdusse, A. / Menetrey, J. | ||||||
Citation | Journal: Embo J. / Year: 2009 Title: The Structural Basis of Arf Effector Specificity: The Crystal Structure of Arf6 in a Complex with Jip4. Authors: Isabet, T. / Montagnac, G. / Regazzoni, K. / Raynal, B. / El Khadali, F. / England, P. / Franco, M. / Chavrier, P. / Houdusse, A. / Menetrey, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2w83.cif.gz | 147.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2w83.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 2w83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w83_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2w83_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2w83_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 2w83_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/2w83 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/2w83 | HTTPS FTP |
-Related structure data
Related structure data | 2j5xS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 2 types, 5 molecules ABECD
#1: Protein | Mass: 18990.822 Da / Num. of mol.: 3 / Fragment: G DOMAIN, RESIDUES 13-175 / Mutation: YES Source method: isolated from a genetically manipulated source Details: 12 RESIDUES N-TERMINAL DELETION / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P62330 #2: Protein | Mass: 8878.157 Da / Num. of mol.: 2 / Fragment: LEUCINE ZIPPER II, RESIDUES 392-462 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60271 |
---|
-Non-polymers , 5 types, 287 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-DIO / #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
---|
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, GLN 67 TO LEU ENGINEERED RESIDUE IN CHAIN B, GLN 67 TO LEU ...ENGINEERED |
---|---|
Sequence details | RTEV PROTEASE SITE REMAINING LINKER: RESIDUES 11-12 IN CHAINS A, B & E, AND RESIDUES 386-391 IN CHAINS C & D. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.56 % / Description: NONE |
---|---|
Crystal grow | Details: 2.0 M AMONIUM SULFATE, 0.1 M HEPES PH 7.5, 0.2 M NACL, 2 MM MGCL2, 6 % MPD |
-Data collection
Diffraction | Mean temperature: 287 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.1271 |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Apr 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→35 Å / Num. obs: 62165 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.93→2.03 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / % possible all: 98.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J5X Resolution: 1.93→118.68 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.811 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN B, RESIDUES 91-97 AND 129-137 ARE DISORDERED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.43 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→118.68 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|