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Yorodumi- PDB-3f1j: Crystal structure of the Borna disease virus matrix protein (BDV-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f1j | ||||||
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Title | Crystal structure of the Borna disease virus matrix protein (BDV-M) reveals RNA binding properties | ||||||
Components | Matrix proteinViral matrix protein | ||||||
Keywords | VIRAL PROTEIN / Viral matrix protein / RNA binding / membrane binding / Viruses / ssRNA negative-strand viruses / Mononegavirales / Bornaviridae / Bornavirus / Alternative splicing / Cytoplasm / Virion | ||||||
Function / homology | Function and homology information virion component => GO:0044423 / virion component / host cell cytoplasm / structural constituent of virion / host cell plasma membrane / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Borna disease virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å | ||||||
Authors | Neumann, P. / Lieber, D. / Meyer, S. / Dautel, P. / Kerth, A. / Kraus, I. / Garten, W. / Stubbs, M.T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Crystal structure of the Borna disease virus matrix protein (BDV-M) reveals ssRNA binding properties Authors: Neumann, P. / Lieber, D. / Meyer, S. / Dautel, P. / Kerth, A. / Kraus, I. / Garten, W. / Stubbs, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f1j.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f1j.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 3f1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/3f1j ftp://data.pdbj.org/pub/pdb/validation_reports/f1/3f1j | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16371.610 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borna disease virus / Gene: M / Plasmid: pMAL-c2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P52637, UniProt: P0C794*PLUS | ||
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#2: Chemical | ChemComp-C5P / | ||
#3: Chemical | #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: 3.77 Å3/Da / Density % sol: 67.34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% PEG 8000, 0.5M Li2SO4, 0.1M Tris/HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.9500, 0.97920, 0.97950 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Feb 20, 2002 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Number: 59411 / Rmerge(I) obs: 0.091 / D res high: 2.59 Å / Num. obs: 14675 / % possible obs: 98.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.65→20 Å / Num. all: 7660 / Num. obs: 7570 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.46 % / Biso Wilson estimate: 67.809 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.099 / Net I/σ(I): 11.97 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.65→2.8 Å / Redundancy: 7.68 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 3.1 / Num. measured obs: 8630 / Num. unique all: 1133 / Num. unique obs: 1123 / Rsym value: 0.671 / % possible all: 99.1 |
-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.65→19.54 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.836 / Data cutoff high absF: 11301727 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.411 Å2 / ksol: 0.297 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.19 Å2 / Biso mean: 61.819 Å2 / Biso min: 35.38 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→19.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.77 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 8
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Xplor file |
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