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- PDB-1vg0: The crystal structures of the REP-1 protein in complex with monop... -
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Open data
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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 | ||||||
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![]() | PROTEIN BINDING/PROTEIN TRANSPORT / RAB PRENYLATION / POST-TRANSLATIONAL MODIFICATION / PROTEIN BINDING-PROTEIN TRANSPORT COMPLEX | ||||||
Function / homology | ![]() RAB GEFs exchange GTP for GDP on RABs / RHOF GTPase cycle / TBC/RABGAPs / RHOD GTPase cycle / lipophagy / RHOG GTPase cycle / positive regulation of viral process / phagosome acidification / RAC2 GTPase cycle / RHOH GTPase cycle ...RAB GEFs exchange GTP for GDP on RABs / RHOF GTPase cycle / TBC/RABGAPs / RHOD GTPase cycle / lipophagy / RHOG GTPase cycle / positive regulation of viral process / phagosome acidification / 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 / MHC class II antigen presentation / protein geranylgeranylation / endosome to plasma membrane protein transport / 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 / GDP-dissociation inhibitor activity / protein targeting to membrane / 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 / response to bacterium / intracellular protein transport / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rak, A. / Pylypenko, O. / Niculae, A. / Pyatkov, K. / Goody, R.S. / Alexandrov, K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.5 KB | Display | ![]() |
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PDB format | ![]() | 121.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 976.2 KB | Display | ![]() |
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Full document | ![]() | 989.4 KB | Display | |
Data in XML | ![]() | 31.1 KB | Display | |
Data in CIF | ![]() | 45.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vg1C ![]() 1vg8C ![]() 1vg9C ![]() 1ltxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() |
-Non-polymers , 6 types, 443 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/GER.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GER.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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