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Yorodumi- PDB-3sfv: Crystal structure of the GDP-bound Rab1a S25N mutant in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sfv | ||||||
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Title | Crystal structure of the GDP-bound Rab1a S25N mutant in complex with the coiled-coil domain of LidA from Legionella pneumophila | ||||||
Components |
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Keywords | protein transport/protein binding / LidA-Rab Complex / Coiled-coil domain / Type IV effector protein from legionella / GDP Binding / protein transport-protein binding complex | ||||||
Function / homology | Function and homology information positive regulation of glycoprotein metabolic process / growth hormone secretion / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic ...positive regulation of glycoprotein metabolic process / growth hormone secretion / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / transport vesicle membrane / virion assembly / Golgi organization / autophagosome assembly / endomembrane system / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / vesicle-mediated transport / substrate adhesion-dependent cell spreading / small monomeric GTPase / G protein activity / positive regulation of interleukin-8 production / intracellular protein transport / autophagy / endocytosis / melanosome / cell migration / early endosome / defense response to bacterium / cadherin binding / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Yin, K. / Lu, D. / Zhu, D. / Zhang, H. / Li, B. / Xu, S. / Gu, L. | ||||||
Citation | Journal: Plos Pathog. / Year: 2012 Title: Structural Insights into a Unique Legionella pneumophila Effector LidA Recognizing Both GDP and GTP Bound Rab1 in Their Active State Authors: Cheng, W. / Yin, K. / Lu, D. / Li, B. / Zhu, D. / Chen, Y. / Zhang, H. / Xu, S. / Chai, J. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sfv.cif.gz | 128.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sfv.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 3sfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sfv_validation.pdf.gz | 792.5 KB | Display | wwPDB validaton report |
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Full document | 3sfv_full_validation.pdf.gz | 795.9 KB | Display | |
Data in XML | 3sfv_validation.xml.gz | 24 KB | Display | |
Data in CIF | 3sfv_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/3sfv ftp://data.pdbj.org/pub/pdb/validation_reports/sf/3sfv | HTTPS FTP |
-Related structure data
Related structure data | 3tklC 2folS 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
#1: Protein | Mass: 20466.213 Da / Num. of mol.: 1 / Fragment: residues 1-176 / Mutation: S25N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1A / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62820 |
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#2: Protein | Mass: 40201.562 Da / Num. of mol.: 1 / Fragment: Coiled-coil domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Corby / Gene: lidA / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5IFX1 |
#3: Chemical | ChemComp-GDP / |
#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: 2.15 Å3/Da / Density % sol: 42.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 28% Jeffamin ED-2001, 0.1M sodium citrate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 24, 2010 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→50 Å / Num. all: 55418 / Num. obs: 55418 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.73→1.79 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 5.42 / Num. unique all: 5457 / Rsym value: 0.359 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 2FOL Resolution: 1.73→50 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.18 / σ(F): 0 / σ(I): 0 / Phase error: 22.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.134 Å2 / ksol: 0.365 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.88 Å2 / Biso mean: 24.07 Å2 / Biso min: 10.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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