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Yorodumi- PDB-5i72: Crystal structure of the oligomeric form of the Lassa virus matri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i72 | ||||||
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Title | Crystal structure of the oligomeric form of the Lassa virus matrix protein Z | ||||||
Components | RING finger protein Z | ||||||
Keywords | VIRAL PROTEIN / arenavirus / Lassa virus / matrix / Z / oligomer | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / viral budding from plasma membrane / virion component / host cell perinuclear region of cytoplasm / host cell plasma membrane / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Lassa virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Hastie, K. / Zandonatti, M. / Liu, T. / Li, S. / Woods Jr, V. / Saphire, E.O. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Virol. / Year: 2016 Title: Crystal Structure of the Oligomeric Form of Lassa Virus Matrix Protein Z. Authors: Hastie, K.M. / Zandonatti, M. / Liu, T. / Li, S. / Woods, V.L. / 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 | 5i72.cif.gz | 35.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i72.ent.gz | 23 KB | Display | PDB format |
PDBx/mmJSON format | 5i72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i72_validation.pdf.gz | 433.9 KB | Display | wwPDB validaton report |
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Full document | 5i72_full_validation.pdf.gz | 434.4 KB | Display | |
Data in XML | 5i72_validation.xml.gz | 6 KB | Display | |
Data in CIF | 5i72_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/5i72 ftp://data.pdbj.org/pub/pdb/validation_reports/i7/5i72 | HTTPS FTP |
-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: 6085.327 Da / Num. of mol.: 2 / Fragment: unp residues 25-77 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lassa virus (strain Mouse/Sierra Leone/Josiah/1976) Strain: Mouse/Sierra Leone/Josiah/1976 / Production host: Escherichia coli (E. coli) / References: UniProt: O73557 #2: Chemical | ChemComp-ZN / |
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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: 4.49 Å3/Da / Density % sol: 72.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 300-400mM ammonium sulfate, 100mM HEPES pH 7.5 and 17% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.2827 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: 3 x 3 CCD array (ADSC Q315R) / Detector: CCD / Date: Feb 10, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2827 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→38.221 Å / Num. obs: 9325 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 86.73 Å2 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.083 / Χ2: 0.93 / Net I/σ(I): 10.2 / Num. measured all: 47129 / Scaling rejects: 2357 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9→38.221 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0.94 / Phase error: 25.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 162.25 Å2 / Biso mean: 89.7017 Å2 / Biso min: 52.25 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→38.221 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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