+Open data
-Basic information
Entry | Database: PDB / ID: 8faq | ||||||||||||
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Title | Structure of Hemagglutinin from Influenza A/Victoria/22/2020 | ||||||||||||
Components | Hemagglutinin | ||||||||||||
Keywords | VIRAL PROTEIN / Influenza A hemagglutinin | ||||||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / 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: 2.035 Å | ||||||||||||
Authors | Hernandez Garcia, A. / Lei, R. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Structure of Hemagglutinin from Influenza A/Victoria/22/2020 Authors: Hernandez Garcia, A. / Lei, R. / Nair, S.K. / Wu, N. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8faq.cif.gz | 121 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8faq.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 8faq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8faq_validation.pdf.gz | 804.7 KB | Display | wwPDB validaton report |
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Full document | 8faq_full_validation.pdf.gz | 808.9 KB | Display | |
Data in XML | 8faq_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 8faq_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/8faq ftp://data.pdbj.org/pub/pdb/validation_reports/fa/8faq | HTTPS FTP |
-Related structure data
Related structure data | 2yp4S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55413.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Victoria/22/2020 / Gene: HA / Cell (production host): sf9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A6M4ZXR4 | ||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.7 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 50% PEG-200, 0.1M citrate pH 5.5, final pH 6.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 3, 2021 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12723 Å / Relative weight: 1 |
Reflection | Resolution: 2.035→79.252 Å / Num. obs: 48446 / % possible obs: 98.6 % / Redundancy: 20.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.079 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.035→2.071 Å / Rmerge(I) obs: 1.642 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2360 / CC1/2: 0.865 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YP4 Resolution: 2.035→79.252 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.209 / SU B: 4.229 / SU ML: 0.112 / Average fsc free: 0.8914 / Average fsc work: 0.9087 / Cross valid method: NONE / ESU R: 0.156 / ESU R Free: 0.142 / Details: Hydrogens have not been used
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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: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.981 Å2
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Refinement step | Cycle: LAST / Resolution: 2.035→79.252 Å
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Refine LS restraints |
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LS refinement shell |
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