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Yorodumi- PDB-4n8c: Three-dimensional structure of the extracellular domain of Matrix... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n8c | ||||||
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Title | Three-dimensional structure of the extracellular domain of Matrix protein 2 of influenza A virus | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody-peptide complex / Influenza A virus protein | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Cho, K.J. / Seok, J.H. / Kim, S. / Roose, K. / Schepens, B. / Fiers, W. / Saelens, X. / Kim, K.H. | ||||||
Citation | Journal: J.Virol. / Year: 2015 Title: Structure of the extracellular domain of matrix protein 2 of influenza A virus in complex with a protective monoclonal antibody Authors: Cho, K.J. / Schepens, B. / Seok, J.H. / Kim, S. / Roose, K. / Lee, J.H. / Gallardo, R. / Hamme, E.V. / Schymkowitz, J. / Rousseau, F. / Fiers, W. / Saelens, X. / Kim, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n8c.cif.gz | 202.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n8c.ent.gz | 159.9 KB | Display | PDB format |
PDBx/mmJSON format | 4n8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/4n8c ftp://data.pdbj.org/pub/pdb/validation_reports/n8/4n8c | HTTPS FTP |
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-Related structure data
Related structure data | 3gbmS 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23861.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #2: Antibody | Mass: 24404.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #3: Protein/peptide | Mass: 2642.940 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This sequence occurs naturally in influenza A virus Source: (synth.) Influenza A virus (A/Puerto Rico/8/1934(H1N1)) #4: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. | |
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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: 2.18 Å3/Da / Density % sol: 43.66 % / Mosaicity: 0.296 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG3350, 200 mM Sodium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. all: 113047 / Num. obs: 109543 / % possible obs: 96.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.054 / Χ2: 0.983 / Net I/σ(I): 13.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GBM Resolution: 1.6→38.43 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.204 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 125.44 Å2 / Biso mean: 27.2785 Å2 / Biso min: 10.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→38.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.643 Å / Total num. of bins used: 20
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