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Yorodumi- PDB-3mlh: Crystal structure of the 2009 H1N1 influenza virus hemagglutinin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mlh | ||||||
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Title | Crystal structure of the 2009 H1N1 influenza virus hemagglutinin receptor-binding domain | ||||||
Components | Hemagglutinin | ||||||
Keywords | VIRAL PROTEIN / hemagglutinin / receptor-binding domain / lectin / antigen | ||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å | ||||||
Authors | DuBois, R.M. / Aguilar-Yanez, J.M. / Mendoza-Ochoa, G.I. / Schultz-Cherry, S. / Alvarez, M.M. / White, S.W. / Russell, C.J. | ||||||
Citation | Journal: J.Virol. / Year: 2011 Title: The Receptor-Binding Domain of Influenza Virus Hemagglutinin Produced in Escherichia coli Folds into Its Native, Immunogenic Structure. Authors: Dubois, R.M. / Aguilar-Yanez, J.M. / Mendoza-Ochoa, G.I. / Oropeza-Almazan, Y. / Schultz-Cherry, S. / Alvarez, M.M. / White, S.W. / Russell, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mlh.cif.gz | 178.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mlh.ent.gz | 141.8 KB | Display | PDB format |
PDBx/mmJSON format | 3mlh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mlh_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 3mlh_full_validation.pdf.gz | 444.4 KB | Display | |
Data in XML | 3mlh_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 3mlh_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/3mlh ftp://data.pdbj.org/pub/pdb/validation_reports/ml/3mlh | HTTPS FTP |
-Related structure data
Related structure data | 1ruyS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26414.424 Da / Num. of mol.: 2 / Fragment: receptor-binding domain (UNP residues 63-286) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Mexico/4603/2009(H1N1) / Gene: HA / Plasmid: pJexpress404 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 strain / References: UniProt: C4RSQ3 #2: Chemical | ChemComp-GOL / #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: 2.09 Å3/Da / Density % sol: 41.24 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 2000MME, Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. all: 25593 / Num. obs: 25588 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 12.73 / Redundancy: 5 % / Biso Wilson estimate: 19.628 Å2 / Rmerge(I) obs: 0.127 / Χ2: 1.147 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.83 / Num. unique all: 2518 / Χ2: 1.123 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 44.07 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1RUY Resolution: 2.09→39.72 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.233 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
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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 max: 43.65 Å2 / Biso mean: 19.628 Å2 / Biso min: 5.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→39.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.144 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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