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Yorodumi- PDB-5v7b: Crystal structure of Influenza A virus matrix protein M1 (NLS-88E) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v7b | |||||||||
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Title | Crystal structure of Influenza A virus matrix protein M1 (NLS-88E) | |||||||||
Components | Matrix protein 1 | |||||||||
Keywords | VIRAL PROTEIN / Influenza A / Matrix protein / NLS-88E mutant / pH 7.0 | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / structural constituent of virion / host cell nucleus / virion membrane / RNA binding / membrane Similarity search - Function | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Musayev, F.N. / Safo, M.K. / Desai, U.R. / Xie, H. / Mosier, P.D. / Chiang, M.-J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Emerg Microbes Infect / Year: 2017 Title: Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. Authors: Chiang, M.J. / Musayev, F.N. / Kosikova, M. / Lin, Z. / Gao, Y. / Mosier, P.D. / Althufairi, B. / Ye, Z. / Zhou, Q. / Desai, U.R. / Xie, H. / Safo, M.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v7b.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v7b.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 5v7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/5v7b ftp://data.pdbj.org/pub/pdb/validation_reports/v7/5v7b | HTTPS FTP |
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-Related structure data
Related structure data | 5v6gC 5v7sC 5v8aC 1ea3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19069.975 Da / Num. of mol.: 2 / Mutation: G88E, R101S, R105S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Wilson-Smith/1933 H1N1) Strain: A/Wilson-Smith/1933 H1N1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Nico21 (DE3) / References: UniProt: P05777 #2: 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: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 7 Details: 16.7 mg/ml protein in 25mM Hepes/NaOH, 0.2M NaCl, 2mM TCEP, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 8, 2013 / Details: Rigaku varimax confocal |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→27.91 Å / Num. obs: 12404 / % possible obs: 98.7 % / Redundancy: 3.57 % / Biso Wilson estimate: 64.7 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1227 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EA3 Resolution: 2.5→27.58 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1093448.38 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 47.3599 Å2 / ksol: 0.311801 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61 Å2
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Refine analyze |
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Refinement step | Cycle: 1 / Resolution: 2.5→27.58 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 10
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