+Open data
-Basic information
Entry | Database: PDB / ID: 1huq | ||||||
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Title | 1.8A CRYSTAL STRUCTURE OF THE MONOMERIC GTPASE RAB5C (MOUSE) | ||||||
Components | RAB5C | ||||||
Keywords | PROTEIN TRANSPORT / G-protein / GTP hydrolysis / endocytosis / Rab protein / membrane trafficking | ||||||
Function / homology | Function and homology information RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / plasma membrane to endosome transport / Golgi Associated Vesicle Biogenesis / endosome organization / Clathrin-mediated endocytosis / regulation of endocytosis / endocytic vesicle / endomembrane system / Neutrophil degranulation ...RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / plasma membrane to endosome transport / Golgi Associated Vesicle Biogenesis / endosome organization / Clathrin-mediated endocytosis / regulation of endocytosis / endocytic vesicle / endomembrane system / Neutrophil degranulation / lipid droplet / small monomeric GTPase / G protein activity / intracellular protein transport / synaptic vesicle membrane / endocytosis / GDP binding / melanosome / early endosome membrane / endosome / GTPase activity / GTP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Merithew, E. / Hatherly, S. / Dumas, J.J. / Lawe, D.C. / Heller-Harrison, R. / Lambright, D.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Structural plasticity of an invariant hydrophobic triad in the switch regions of Rab GTPases is a determinant of effector recognition. Authors: Merithew, E. / Hatherly, S. / Dumas, J.J. / Lawe, D.C. / Heller-Harrison, R. / Lambright, D.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1huq.cif.gz | 52.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1huq.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 1huq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/1huq ftp://data.pdbj.org/pub/pdb/validation_reports/hu/1huq | HTTPS FTP |
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-Related structure data
Related structure data | 3rabS S: Starting model for refinement |
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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
#1: Protein | Mass: 18273.828 Da / Num. of mol.: 1 / Fragment: GTPASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P35278 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GNP / |
#4: 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: 2.07 Å3/Da / Density % sol: 40.54 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG-6000, sodium chloride, magnesium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 35 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2000 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 14494 / Num. obs: 14494 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 15.5 Å2 / Rsym value: 0.054 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 1125 / Rsym value: 0.227 / % possible all: 94.9 |
Reflection | *PLUS Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 94.9 % / Rmerge(I) obs: 0.227 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RAB Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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