+Open data
-Basic information
Entry | Database: PDB / ID: 4fmb | ||||||
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Title | VirA-Rab1 complex structure | ||||||
Components |
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Keywords | PROTEIN BINDING / alpha-beta fold / Rab1-GAP complex / Rab1 | ||||||
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 / virion assembly / transport vesicle membrane / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / 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 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / early endosome / defense response to bacterium / cadherin binding / cysteine-type endopeptidase activity / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / proteolysis / extracellular exosome / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | Shigella flexneri (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Shao, F. / Zhu, Y. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2012 Title: Structurally Distinct Bacterial TBC-like GAPs Link Arf GTPase to Rab1 Inactivation to Counteract Host Defenses. Authors: Dong, N. / Zhu, Y. / Lu, Q. / Hu, L. / Zheng, Y. / Shao, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fmb.cif.gz | 309 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fmb.ent.gz | 257.2 KB | Display | PDB format |
PDBx/mmJSON format | 4fmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/4fmb ftp://data.pdbj.org/pub/pdb/validation_reports/fm/4fmb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 40140.234 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 301 / Gene: CP0181, pWR501_0191, virA / Plasmid: pGEX-6p-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7BU69, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Protein | Mass: 19384.988 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1, RAB1A / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62820 |
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-Non-polymers , 4 types, 18 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUES WERE CONFIRMED BY GENE SEQUENCING |
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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: 3.55 Å3/Da / Density % sol: 65.35 % |
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Crystal grow | Temperature: 298 K / pH: 7.6 Details: 0.8 M ammonium sulfate and 0.1 M Tris-HCl (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2011 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 40511 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 55.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 105.24 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.31 Å / Total num. of bins used: 10
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Xplor file |
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