+Open data
-Basic information
Entry | Database: PDB / ID: 7a9d | ||||||
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Title | Crystal structure of H12 Haemagglutinin | ||||||
Components | (Hemagglutinin) x 2 | ||||||
Keywords | VIRAL PROTEIN / receptor binding / fusion of virus membrane with host plasma membrane. | ||||||
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 / Resolution: 2.7 Å | ||||||
Authors | Xiong, X. / Walker, P. / Zhang, J. / Gamblin, S. / Skehel, J.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Cold Spring Harb Perspect Med / Year: 2021 Title: Hemagglutinin Structure and Activities. Authors: Gamblin, S.J. / Vachieri, S.G. / Xiong, X. / Zhang, J. / Martin, S.R. / Skehel, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a9d.cif.gz | 203.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a9d.ent.gz | 163.5 KB | Display | PDB format |
PDBx/mmJSON format | 7a9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a9d_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7a9d_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7a9d_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 7a9d_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/7a9d ftp://data.pdbj.org/pub/pdb/validation_reports/a9/7a9d | HTTPS FTP |
-Related structure data
Related structure data | 6zrkC 1jsdS S: Starting model for refinement C: citing same article (ref.) |
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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: Protein | Mass: 36392.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/duck/Alberta/60/1976(H12N5)) Gene: HA / Cell line (production host): Sf9 / Production host: unidentified baculovirus / References: UniProt: C6KJK3, UniProt: P03446*PLUS #2: Protein | Mass: 19094.072 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/duck/Alberta/60/1976(H12N5)) Gene: HA / Cell line (production host): Sf9 / Production host: unidentified baculovirus / References: UniProt: P03446 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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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: 3.4 Å3/Da / Density % sol: 63.3 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.0, 30% Jeffamine ED2001 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→89.75 Å / Num. obs: 39909 / % possible obs: 97.1 % / Redundancy: 6.5 % / CC1/2: 0.995 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.7→2.85 Å / Num. unique obs: 5872 / CC1/2: 0.808 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1jsd Resolution: 2.7→89.75 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.814 / ESU R Free: 0.383 / 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: 150.62 Å2 / Biso mean: 72.9468 Å2 / Biso min: 32.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→89.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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