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- PDB-5dup: Influenza A virus H5 hemagglutinin globular head in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dup | ||||||
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Title | Influenza A virus H5 hemagglutinin globular head in complex with antibody AVFluIgG03 | ||||||
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![]() | IMMUNE SYSTEM / Influenza virus / Antibody / Complex / Neutralize | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zuo, T. / Sun, J. / Wang, G. / Zhou, P. / Wang, X. / Zhang, L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241.8 KB | Display | ![]() |
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PDB format | ![]() | 201.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.1 KB | Display | ![]() |
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Full document | ![]() | 469.5 KB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 26535.771 Da / Num. of mol.: 1 / Fragment: globular head, UNP residues 61-284 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Anhui/1/2005(H5N1) / Gene: HA / Cell line (production host): SF9 / Production host: ![]() ![]() |
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#2: Antibody | Mass: 24784.436 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Antibody | Mass: 22859.150 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 63.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→38.94 Å / Num. obs: 16857 / % possible obs: 100 % / Redundancy: 7.2 % / Net I/σ(I): 12.1 |
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Processing
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Refinement | Resolution: 3.052→38.938 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.72 / Stereochemistry target values: TWIN_LSQ_F
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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: 3.052→38.938 Å
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Refine LS restraints |
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LS refinement shell |
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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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