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Yorodumi- PDB-5dum: Crystal structure of influenza A virus H5 hemagglutinin globular ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dum | ||||||
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Title | Crystal structure of influenza A virus H5 hemagglutinin globular head in complex with the Fab of antibody 65C6 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / influenza virus / Antibody / Complex / Neutralize | ||||||
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 | Homo sapiens (human) Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.003 Å | ||||||
Authors | Sun, J. / Zuo, T. / Wang, G. / Zhou, P. / Zhang, L. / Wang, X. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Comprehensive analysis of antibody recognition in convalescent humans from highly pathogenic avian influenza H5N1 infection Authors: Zuo, T. / Sun, J. / Wang, G. / Jiang, L. / Zuo, Y. / Li, D. / Shi, X. / Liu, X. / Fan, S. / Ren, H. / Hu, H. / Sun, L. / Zhou, B. / Liang, M. / Zhou, P. / Wang, X. / Zhang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dum.cif.gz | 122.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dum.ent.gz | 97.5 KB | Display | PDB format |
PDBx/mmJSON format | 5dum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dum_validation.pdf.gz | 464.5 KB | Display | wwPDB validaton report |
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Full document | 5dum_full_validation.pdf.gz | 474 KB | Display | |
Data in XML | 5dum_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 5dum_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/5dum ftp://data.pdbj.org/pub/pdb/validation_reports/du/5dum | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 25716.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293T / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23412.010 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293T / Production host: Homo sapiens (human) |
#3: Protein | Mass: 26535.771 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Anhui/1/2005(H5N1)) Strain: A/Anhui/1/2005(H5N1) / Gene: HA / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q1WDM0 |
#4: Sugar |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7 Details: 2% w/v Polyethylene glycol 400, 0.1M Imidazole pH7.0, 24% w/v Polyethylene glycol monomethyl ether 5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 16304 / % possible obs: 99.8 % / Redundancy: 5.8 % / Net I/σ(I): 13.9 |
-Processing
Software |
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Refinement | Resolution: 3.003→36.13 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.16 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.003→36.13 Å
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Refine LS restraints |
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LS refinement shell |
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