+Open data
-Basic information
Entry | Database: PDB / ID: 1t91 | ||||||
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Title | crystal structure of human small GTPase Rab7(GTP) | ||||||
Components | Ras-related protein Rab-7 | ||||||
Keywords | PROTEIN TRANSPORT / small GTPase | ||||||
Function / homology | Function and homology information lipophagy / epidermal growth factor catabolic process / positive regulation of viral process / phagosome acidification / protein to membrane docking / negative regulation of intralumenal vesicle formation / alveolar lamellar body / negative regulation of exosomal secretion / phagosome-lysosome fusion / Suppression of autophagy ...lipophagy / epidermal growth factor catabolic process / positive regulation of viral process / phagosome acidification / protein to membrane docking / negative regulation of intralumenal vesicle formation / alveolar lamellar body / negative regulation of exosomal secretion / phagosome-lysosome fusion / Suppression of autophagy / phagosome maturation / establishment of vesicle localization / retromer complex binding / endosome to plasma membrane protein transport / melanosome membrane / phagophore assembly site membrane / protein targeting to lysosome / RAB geranylgeranylation / early endosome to late endosome transport / positive regulation of exosomal secretion / RAB GEFs exchange GTP for GDP on RABs / RHOF GTPase cycle / RHOD GTPase cycle / retrograde transport, endosome to Golgi / TBC/RABGAPs / endosome to lysosome transport / RHOJ GTPase cycle / RHOQ GTPase cycle / autophagosome membrane / RHOH GTPase cycle / autophagosome assembly / CDC42 GTPase cycle / intracellular transport / RHOG GTPase cycle / viral release from host cell / RAC3 GTPase cycle / RAC2 GTPase cycle / lipid catabolic process / phagocytic vesicle / bone resorption / Prevention of phagosomal-lysosomal fusion / RAC1 GTPase cycle / MHC class II antigen presentation / lipid droplet / small monomeric GTPase / G protein activity / secretory granule membrane / mitochondrial membrane / response to bacterium / synaptic vesicle membrane / small GTPase binding / endocytosis / phagocytic vesicle membrane / GDP binding / positive regulation of protein catabolic process / protein transport / late endosome / late endosome membrane / lysosome / endosome membrane / lysosomal membrane / GTPase activity / Neutrophil degranulation / GTP binding / Golgi apparatus / mitochondrion / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Song, H. / Hong, W. / Wu, M. / Wang, T. | ||||||
Citation | Journal: Embo J. / Year: 2005 Title: Structural basis for recruitment of RILP by small GTPase Rab7. Authors: Wu, M. / Wang, T. / Loh, E. / Hong, W. / Song, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t91.cif.gz | 164.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t91.ent.gz | 129.6 KB | Display | PDB format |
PDBx/mmJSON format | 1t91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/1t91 ftp://data.pdbj.org/pub/pdb/validation_reports/t9/1t91 | HTTPS FTP |
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-Related structure data
Related structure data | 1yhnC 1huqS 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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Unit cell |
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-Components
#1: Protein | Mass: 23501.748 Da / Num. of mol.: 4 / Mutation: Q67L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Rab7 / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Star / References: UniProt: P51149 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GTP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: polyethylene glycol monomethyl ether 2000, ammonium sulfate, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9722 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 2, 2004 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9722 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→33.049 Å / Num. all: 63332 / Num. obs: 61851 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.059 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.8 % / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: mouse rab5c, 1HUQ Resolution: 1.9→20 Å / σ(F): 2 / σ(I): 2
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Solvent computation | Solvent model: MAXIMUM LIKELIHOOD | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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