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Yorodumi- PDB-1vg0: The crystal structures of the REP-1 protein in complex with monop... -
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-Basic information
Entry | Database: PDB / ID: 1vg0 | ||||||
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Title | The crystal structures of the REP-1 protein in complex with monoprenylated Rab7 protein | ||||||
Components |
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Keywords | PROTEIN BINDING/PROTEIN TRANSPORT / RAB PRENYLATION / POST-TRANSLATIONAL MODIFICATION / PROTEIN BINDING-PROTEIN TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information RAB GEFs exchange GTP for GDP on RABs / RHOF GTPase cycle / TBC/RABGAPs / : / RHOD GTPase cycle / lipophagy / positive regulation of viral process / phagosome acidification / RHOG GTPase cycle / RAC2 GTPase cycle ...RAB GEFs exchange GTP for GDP on RABs / RHOF GTPase cycle / TBC/RABGAPs / : / RHOD GTPase cycle / lipophagy / positive regulation of viral process / phagosome acidification / RHOG GTPase cycle / RAC2 GTPase cycle / RHOH GTPase cycle / protein to membrane docking / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / RHOQ GTPase cycle / epidermal growth factor catabolic process / RAB geranylgeranylation / RAC1 GTPase cycle / Rab-protein geranylgeranyltransferase complex / alveolar lamellar body / negative regulation of exosomal secretion / phagosome-lysosome fusion / establishment of vesicle localization / retromer complex binding / endosome to plasma membrane protein transport / MHC class II antigen presentation / protein geranylgeranylation / retromer complex / melanosome membrane / phagophore assembly site membrane / protein targeting to lysosome / early endosome to late endosome transport / positive regulation of exosomal secretion / retrograde transport, endosome to Golgi / protein targeting to membrane / GDP-dissociation inhibitor activity / Neutrophil degranulation / small GTPase-mediated signal transduction / endosome to lysosome transport / blood vessel development / autophagosome membrane / autophagosome assembly / viral release from host cell / intracellular transport / lipid catabolic process / vesicle-mediated transport / bone resorption / phagocytic vesicle / lipid droplet / GTPase activator activity / small monomeric GTPase / G protein activity / mitochondrial membrane / intracellular protein transport / response to bacterium / terminal bouton / synaptic vesicle membrane / small GTPase binding / positive regulation of protein catabolic process / phagocytic vesicle membrane / GDP binding / late endosome / late endosome membrane / lysosome / endosome membrane / endosome / lysosomal membrane / GTPase activity / protein-containing complex binding / GTP binding / Golgi apparatus / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Rak, A. / Pylypenko, O. / Niculae, A. / Pyatkov, K. / Goody, R.S. / Alexandrov, K. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2004 Title: Structure of the Rab7:REP-1 complex: insights into the mechanism of Rab prenylation and choroideremia disease Authors: Rak, A. / Pylypenko, O. / Niculae, A. / Pyatkov, K. / Goody, R.S. / Alexandrov, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vg0.cif.gz | 162.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vg0.ent.gz | 121.9 KB | Display | PDB format |
PDBx/mmJSON format | 1vg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/1vg0 ftp://data.pdbj.org/pub/pdb/validation_reports/vg/1vg0 | HTTPS FTP |
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-Related structure data
Related structure data | 1vg1C 1vg8C 1vg9C 1ltxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 72622.234 Da / Num. of mol.: 1 / Mutation: K231Q, K462R, T473A, A483G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P37727 |
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#2: Protein | Mass: 23530.744 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09527 |
-Non-polymers , 6 types, 443 molecules
#3: Chemical | ChemComp-CL / |
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#4: Chemical | ChemComp-GER / |
#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-GDP / |
#7: Chemical | ChemComp-PG4 / |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 23% PEG 3350, 0.4M diAmmonium Tartrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2002 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→18 Å / Num. all: 45399 / Num. obs: 45399 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.081 / Net I/σ(I): 10.19 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.61 / Num. unique all: 5630 / Rsym value: 0.357 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: REP-1 from RabGGTase:REP-1 complex (PDB code 1LTX) Resolution: 2.2→18 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2781170.14 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.7874 Å2 / ksol: 0.325713 e/Å3 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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