+Open data
-Basic information
Entry | Database: PDB / ID: 3zp2 | |||||||||
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Title | INFLUENZA VIRUS (VN1194) H5 HA A138V mutant with LSTa | |||||||||
Components | (HAEMAGGLUTININ) 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. / 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 | 3zp2.cif.gz | 201.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zp2.ent.gz | 167 KB | Display | PDB format |
PDBx/mmJSON format | 3zp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zp2_validation.pdf.gz | 778.8 KB | Display | wwPDB validaton report |
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Full document | 3zp2_full_validation.pdf.gz | 788 KB | Display | |
Data in XML | 3zp2_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 3zp2_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/3zp2 ftp://data.pdbj.org/pub/pdb/validation_reports/zp/3zp2 | HTTPS FTP |
-Related structure data
Related structure data | 3zp0C 3zp1C 3zp3C 3zp6C 3zpaC 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: 37062.988 Da / Num. of mol.: 1 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-342 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS / Strain: VIETNAM/1194/2004 (H5N1) Description: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC) Variant: VN/1194/04/NIBRG14 VACCINE STRAIN / Organ (production host): EGG / Production host: GALLUS GALLUS (chicken) / References: UniProt: Q6DQ34 | ||
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#2: Protein | Mass: 19097.990 Da / Num. of mol.: 1 Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS / Strain: VIETNAM/1194/2004 (H5N1) Description: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC) Variant: VN/1194/04/NIBRG14 VACCINE STRAIN / Organ (production host): EGG / Production host: GALLUS GALLUS (chicken) / References: UniProt: Q6DQ34 | ||
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source | ||
#4: Sugar | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.79 % / 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: 31234 / % possible obs: 100 % / Observed criterion σ(I): 3.8 / Redundancy: 10.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.6 |
-Processing
Software | Name: REFMAC / Version: 5.5.0088 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.126 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES WITH TLS ADDED
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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: 54.337 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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