+Open data
-Basic information
Entry | Database: PDB / ID: 5b0v | ||||||
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Title | Crystal Structure of Marburg virus VP40 Dimer | ||||||
Components | Matrix protein VP40 | ||||||
Keywords | VIRAL PROTEIN / Marburg virus / virus assembly protein / immunosuppression / filovirus | ||||||
Function / homology | Function and homology information host cell endomembrane system / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / host cell late endosome membrane / viral budding via host ESCRT complex / viral budding from plasma membrane / structural constituent of virion / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell plasma membrane / virion membrane Similarity search - Function | ||||||
Biological species | Lake Victoria marburgvirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.81 Å | ||||||
Authors | Oda, S. / Bornholdt, Z.A. / Abelson, D.M. / Saphire, E.O. | ||||||
Citation | Journal: J.Virol. / Year: 2015 Title: Crystal Structure of Marburg Virus VP40 Reveals a Broad, Basic Patch for Matrix Assembly and a Requirement of the N-Terminal Domain for Immunosuppression Authors: Oda, S. / Noda, T. / Wijesinghe, K.J. / Halfmann, P. / Bornholdt, Z.A. / Abelson, D.M. / Armbrust, T. / Stahelin, R.V. / Kawaoka, Y. / Saphire, E.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b0v.cif.gz | 212.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b0v.ent.gz | 176.9 KB | Display | PDB format |
PDBx/mmJSON format | 5b0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/5b0v ftp://data.pdbj.org/pub/pdb/validation_reports/b0/5b0v | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 36017.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lake Victoria marburgvirus (strain Musoke-80) Strain: Musoke-80 / Gene: VP40 / Production host: Escherichia coli (E. coli) / References: UniProt: P35260 #2: Chemical | ChemComp-EOH / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.99 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 17.5% ethanol, 75mM NaCl, 10mM CHAPS, 100mM Tris-HCl, pH 7.7 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979, 0.980 | |||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2012 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.81→50 Å / Num. obs: 25037 / % possible obs: 99.5 % / Redundancy: 4 % / Net I/σ(I): 6.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.81→29.67 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.879 / SU B: 35.489 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.378 Å2
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Refinement step | Cycle: 1 / Resolution: 2.81→29.67 Å
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Refine LS restraints |
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