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Yorodumi- PDB-4xqo: Crystal structure of hemagglutinin from Jiangxi-Donghu (2013) H10... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xqo | |||||||||
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Title | Crystal structure of hemagglutinin from Jiangxi-Donghu (2013) H10N8 influenza virus in complex with 6'-SLN | |||||||||
Components | (Hemagglutinin ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN | |||||||||
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: 2.85 Å | |||||||||
Authors | Tzarum, N. / Zhang, H. / Zhu, X. / Wilson, I.A. | |||||||||
Citation | Journal: Cell Host Microbe / Year: 2015 Title: A Human-Infecting H10N8 Influenza Virus Retains a Strong Preference for Avian-type Receptors. Authors: Zhang, H. / de Vries, R.P. / Tzarum, N. / Zhu, X. / Yu, W. / McBride, R. / Paulson, J.C. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xqo.cif.gz | 295.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xqo.ent.gz | 238.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xqo_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4xqo_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4xqo_validation.xml.gz | 53.1 KB | Display | |
Data in CIF | 4xqo_validation.cif.gz | 71.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/4xqo ftp://data.pdbj.org/pub/pdb/validation_reports/xq/4xqo | HTTPS FTP |
-Related structure data
Related structure data | 4xq5SC 4xquC 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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Unit cell |
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-Components
-Hemagglutinin ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 35682.258 Da / Num. of mol.: 3 / Fragment: residues 18-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Jiangxi/IPB13/2013(H10N8) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A0A059T4A1 #2: Protein | Mass: 20755.818 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Jiangxi/IPB13/2013(H10N8) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A0A059T4A1 |
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-Sugars , 4 types, 6 molecules
#3: Polysaccharide | #4: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine | #5: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | |
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-Non-polymers , 1 types, 27 molecules
#7: 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: 3.06 Å3/Da / Density % sol: 59.8 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M NaSCN, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0716 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0716 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.85→50 Å / Num. obs: 42408 / % possible obs: 89 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.108 / Rrim(I) all: 0.182 / Χ2: 3.278 / Net I/av σ(I): 14.653 / Net I/σ(I): 7.6 / Num. measured all: 108611 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XQ5 Resolution: 2.85→46.168 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 144.48 Å2 / Biso mean: 68.5876 Å2 / Biso min: 26.94 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.85→46.168 Å
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LS refinement shell | Resolution: 2.85→2.9163 Å /
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