+Open data
-Basic information
Entry | Database: PDB / ID: 3cph | ||||||
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Title | Crystal structure of Sec4 in complex with Rab-GDI | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Rab GTPase / prenylation / vesicular transport / Cytoplasm / Cytoplasmic vesicle / Exocytosis / GTP-binding / Lipoprotein / Membrane / Nucleotide-binding / Palmitate / Phosphoprotein / GTPase activation | ||||||
Function / homology | Function and homology information Rab GDP-dissociation inhibitor activity / ascospore-type prospore assembly / membrane addition at site of cytokinesis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / incipient cellular bud site / vesicle fusion / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / cellular bud neck ...Rab GDP-dissociation inhibitor activity / ascospore-type prospore assembly / membrane addition at site of cytokinesis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / incipient cellular bud site / vesicle fusion / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / cellular bud neck / regulation of exocytosis / mating projection tip / transport vesicle membrane / small GTPase-mediated signal transduction / exocytosis / protein secretion / vesicle-mediated transport / transport vesicle / Neutrophil degranulation / GTPase activator activity / protein localization to plasma membrane / autophagy / protein transport / vesicle / mitochondrial outer membrane / endosome / GTPase activity / GTP binding / endoplasmic reticulum / mitochondrion / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Kravchenko, S. / Ignatev, A. / Goody, R.S. / Rak, A. / Pylypenko, O. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism. Authors: Ignatev, A. / Kravchenko, S. / Rak, A. / Goody, R.S. / Pylypenko, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cph.cif.gz | 217.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cph.ent.gz | 173.3 KB | Display | PDB format |
PDBx/mmJSON format | 3cph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/3cph ftp://data.pdbj.org/pub/pdb/validation_reports/cp/3cph | HTTPS FTP |
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-Related structure data
Related structure data | 3cpiC 3cpjC 1ukvS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 51271.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P39958 #2: Protein | | Mass: 23326.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07560 #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-GDP / | #5: 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: 4.34 Å3/Da / Density % sol: 71.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 12% PEG MME 2000, 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: SLS / Beamline: X10SA / Wavelength: 0.9816 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9816 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→19.9 Å / Num. all: 49236 / Num. obs: 48896 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.9→2.95 Å / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ukv, chain G Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU B: 14.504 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.534 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.972 Å / Total num. of bins used: 20
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