+Open data
-Basic information
Entry | Database: PDB / ID: 3zpa | ||||||
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Title | INFLUENZA VIRUS (VN1194) H5 I155F mutant HA | ||||||
Components | (HEMAGGLUTININ) x 2 | ||||||
Keywords | VIRAL PROTEIN | ||||||
Function / homology | Function and homology information 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 Similarity search - Function | ||||||
Biological species | INFLUENZA A VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å | ||||||
Authors | Liu, J. / Chen, Z. / Stevens, D.J. / Gamblin, S.J. / Skehel, J.J. | ||||||
Citation | Journal: Virology / Year: 2013 Title: Changes in the Hemagglutinin of H5N1 Viruses During Human Infection - Influence on Receptor Binding. Authors: Crusat, M. / Liu, J. / Palma, A.S. / Childs, R.A. / Liu, Y. / Wharton, S.A. / Lin, Y.P. / Coombs, P.J. / Martin, S.R. / Matrosovich, M. / Chen, Z. / Stevens, D.J. / Hien, V.M. / Thanh, T.T. ...Authors: Crusat, M. / Liu, J. / Palma, A.S. / Childs, R.A. / Liu, Y. / Wharton, S.A. / Lin, Y.P. / Coombs, P.J. / Martin, S.R. / Matrosovich, M. / Chen, Z. / Stevens, D.J. / Hien, V.M. / Thanh, T.T. / Nhu, L.N.T. / Nguyet, L.A. / Ha, D.Q. / van Doorn, H.R. / Hien, T.T. / Conradt, H.S. / Kiso, M. / Gamblin, S.J. / Chai, W. / Skehel, J.J. / Hay, A.J. / Farrar, J. / De Jong, M.D. / Feizi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zpa.cif.gz | 105.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zpa.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zpa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/3zpa ftp://data.pdbj.org/pub/pdb/validation_reports/zp/3zpa | HTTPS FTP |
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-Related structure data
Related structure data | 3zp0C 3zp1C 3zp2C 3zp3C 3zp6C 3zpbC 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
#1: Protein | Mass: 38556.867 Da / Num. of mol.: 1 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 1-340 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS (A/VIETNAM/1194/2004(H5N1)) Organ (production host): EGG / Production host: GALLUS GALLUS (chicken) / References: UniProt: Q6DQ34 |
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#2: Protein | Mass: 18390.303 Da / Num. of mol.: 1 Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-506 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS (A/VIETNAM/1194/2004(H5N1)) Organ (production host): EGG / Production host: GALLUS GALLUS (chicken) / References: UniProt: Q6DQ34 |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.34 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Type: DIAMOND / Wavelength: 0.9715 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9715 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 27673 / % possible obs: 98.3 % / Observed criterion σ(I): 2.6 / Redundancy: 10.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.3 |
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.89 / SU B: 23.098 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.367 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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