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Yorodumi- PDB-4gha: Crystal structure of Marburg virus VP35 RNA binding domain bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gha | ||||||
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Title | Crystal structure of Marburg virus VP35 RNA binding domain bound to 12-bp dsRNA | ||||||
Components |
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Keywords | VIRAL PROTEIN / RNA BINDING PROTEIN/RNA / Viral polymerase / Interferon inhibition / dsRNA / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Marburg virus - Musoke Kenya 1980 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Bale, S. / Jean-Philippe, J. / Bornholdt, Z.A. / Kimberlin, C.K. / Halfmann, P. / Zandonatti, M.A. / Kunert, J. / Kroon, G.J.A. / Kawaoka, Y. / MacRae, I.J. ...Bale, S. / Jean-Philippe, J. / Bornholdt, Z.A. / Kimberlin, C.K. / Halfmann, P. / Zandonatti, M.A. / Kunert, J. / Kroon, G.J.A. / Kawaoka, Y. / MacRae, I.J. / Wilson, I.A. / Saphire, E.O. | ||||||
Citation | Journal: Plos Pathog. / Year: 2012 Title: Marburg Virus VP35 Can Both Fully Coat the Backbone and Cap the Ends of dsRNA for Interferon Antagonism. Authors: Bale, S. / Julien, J.P. / Bornholdt, Z.A. / Kimberlin, C.R. / Halfmann, P. / Zandonatti, M.A. / Kunert, J. / Kroon, G.J. / Kawaoka, Y. / Macrae, I.J. / Wilson, I.A. / 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 | 4gha.cif.gz | 225.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gha.ent.gz | 178.7 KB | Display | PDB format |
PDBx/mmJSON format | 4gha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gha_validation.pdf.gz | 483.5 KB | Display | wwPDB validaton report |
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Full document | 4gha_full_validation.pdf.gz | 492.3 KB | Display | |
Data in XML | 4gha_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 4gha_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/4gha ftp://data.pdbj.org/pub/pdb/validation_reports/gh/4gha | HTTPS FTP |
-Related structure data
Related structure data | 4gh9SC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 2 / Auth seq-ID: 210 - 325 / Label seq-ID: 27 - 142
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-Components
#1: Protein | Mass: 16302.603 Da / Num. of mol.: 4 Fragment: Marburg virus VP35 RNA binding domain, UNP residues 204-329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marburg virus - Musoke, Kenya, 1980 / Strain: Musoke / Gene: VP35 / Plasmid: pET46b / Production host: Escherichia coli (E. coli) / Strain (production host): R2 / References: UniProt: P35259 #2: RNA chain | Mass: 3812.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA from IDT technologies #3: 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: 2.04 Å3/Da / Density % sol: 39.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris, 2% v/v Tacsimate, 18% PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2011 / Details: Double-crystal, Si(111) liquid N2 cooled |
Radiation | Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→81.8 Å / Num. obs: 20261 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.501→2.566 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.2 / Num. unique all: 988 / Rsym value: 0.362 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GH9 Resolution: 2.5→81.8 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 21.668 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.309 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→81.8 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.501→2.566 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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