+Open data
-Basic information
Entry | Database: PDB / ID: 2j59 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the ARF1:ARHGAP21-ArfBD complex | ||||||
Components |
| ||||||
Keywords | HYDROLASE / ARF / ARF1 / ARFBD / ARHGAP21 / MYRISTATE / TRANSPORT / NUCLEOTIDE-BINDING / RHOGAP PROTEIN / PROTEIN TRANSPORT / ACTIN ORGANIZATION / SMALL GTP-BINDING PROTEIN / GOLGI APPARATUS | ||||||
Function / homology | Function and homology information Glycosphingolipid transport / synaptic vesicle budding / lysosomal membrane organization / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / maintenance of Golgi location / Golgi to transport vesicle transport / trans-Golgi Network Vesicle Budding / phospholipase D activator activity / Synthesis of PIPs at the Golgi membrane ...Glycosphingolipid transport / synaptic vesicle budding / lysosomal membrane organization / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / maintenance of Golgi location / Golgi to transport vesicle transport / trans-Golgi Network Vesicle Budding / phospholipase D activator activity / Synthesis of PIPs at the Golgi membrane / : / Intra-Golgi traffic / Golgi localization / mitotic cleavage furrow ingression / positive regulation of ER to Golgi vesicle-mediated transport / Lysosome Vesicle Biogenesis / COPI-mediated anterograde transport / regulation of receptor internalization / very-low-density lipoprotein particle assembly / regulation of Arp2/3 complex-mediated actin nucleation / Synthesis of PIPs at the plasma membrane / COPI-dependent Golgi-to-ER retrograde traffic / postsynaptic actin cytoskeleton organization / Golgi Associated Vesicle Biogenesis / organelle transport along microtubule / positive regulation of calcium ion-dependent exocytosis / establishment of Golgi localization / MHC class II antigen presentation / RHOF GTPase cycle / dendritic spine organization / RHOD GTPase cycle / anchoring junction / regulation of small GTPase mediated signal transduction / long-term synaptic depression / RND3 GTPase cycle / positive regulation of sodium ion transmembrane transport / RHOB GTPase cycle / positive regulation of dendritic spine development / cell leading edge / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / Golgi organization / positive regulation of endocytosis / CDC42 GTPase cycle / RHOG GTPase cycle / intracellular copper ion homeostasis / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / endomembrane system / vesicle-mediated transport / RAC1 GTPase cycle / sarcomere / GTPase activator activity / small monomeric GTPase / positive regulation of protein secretion / actin filament organization / intracellular protein transport / cytoplasmic vesicle membrane / cellular response to virus / GDP binding / protein transport / actin cytoskeleton / late endosome / cell junction / postsynaptic density / neuron projection / protein domain specific binding / Golgi membrane / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / magnesium ion binding / signal transduction / protein-containing complex / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Menetrey, J. / Perderiset, M. / Cicolari, J. / Dubois, T. / El Khatib, N. / El Khadali, F. / Franco, M. / Chavrier, P. / Houdusse, A. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Structural Basis for Arf1-Mediated Recruitment of Arhgap21 to Golgi Membranes. Authors: Menetrey, J. / Perderiset, M. / Cicolari, J. / Dubois, T. / El Khatib, N. / El Khadali, F. / Franco, M. / Chavrier, P. / Houdusse, A. #1: Journal: Cryst. Growth Des. / Year: 2007 Title: Improving Diffraction from 3A to 2A for a Complex between a Small Gtpase and its Effector by Analysis of Crystal Contacts and Use of Reverse Screening. Authors: Menetrey, J. / Perderiset, M. / Cicolari, J. / Houdusse, A. / Stura, E.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2j59.cif.gz | 389.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2j59.ent.gz | 315 KB | Display | PDB format |
PDBx/mmJSON format | 2j59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j59_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2j59_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 2j59_validation.xml.gz | 81.8 KB | Display | |
Data in CIF | 2j59_validation.cif.gz | 115.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/2j59 ftp://data.pdbj.org/pub/pdb/validation_reports/j5/2j59 | HTTPS FTP |
-Related structure data
Related structure data | 1j2i S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 12 molecules ABCDEFMNOPQR
#1: Protein | Mass: 18951.615 Da / Num. of mol.: 6 / Fragment: DELTA 17-ARF1, RESIDUES 17-180 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P84078 #2: Protein | Mass: 19378.922 Da / Num. of mol.: 6 / Fragment: ARF-BINDING DOMAIN, RESIDUES 929-1096 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8NI19, UniProt: Q5T5U3*PLUS |
---|
-Non-polymers , 6 types, 1680 molecules
#3: Chemical | ChemComp-GTP / #4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-SO4 / #8: Water | ChemComp-HOH / | |
---|
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, GLN 70 TO LEU ENGINEERED RESIDUE IN CHAIN B, GLN 70 TO LEU ...ENGINEERED |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.62 % / Description: NONE |
---|---|
Crystal grow | pH: 6.8 Details: 15 % PEG5000 MME, 100 MM IMIDAZOLE PH 6.8, 150 MM NH4.SO4 OR LI2SO4, 10 MM MGCL2, 0.5 % DIOXANE, 5 % ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 9, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 155860 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.1→2.21 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.8 / % possible all: 95.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J2I 1j2i Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.432 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS 929-930,944-955, 979-986, AND 1064-1096 FROM ARHGAP21-ARFBD WERE OMITTED FROM THE MODEL. RESIDUES FROM THE TAG IN N- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS 929-930,944-955, 979-986, AND 1064-1096 FROM ARHGAP21-ARFBD WERE OMITTED FROM THE MODEL. RESIDUES FROM THE TAG IN N-TERMINUS OF ARF1 (GS) WERE NUMBERED 16 AND 17
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 23.45 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|