+Open data
-Basic information
Entry | Database: PDB / ID: 3zp3 | ||||||
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Title | INFLUENZA VIRUS (VN1194) H5 HA A138V mutant with LSTc | ||||||
Components | (HAEMAGGLUTININHemagglutinin) 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: 2.65 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 | 3zp3.cif.gz | 199.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zp3.ent.gz | 165.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/3zp3 ftp://data.pdbj.org/pub/pdb/validation_reports/zp/3zp3 | HTTPS FTP |
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-Related structure data
Related structure data | 3zp0C 3zp1C 3zp2C 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
-Protein , 2 types, 2 molecules EF
#1: Protein | Mass: 38522.852 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: 18390.303 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 |
-Sugars , 3 types, 4 molecules
#3: Sugar | ChemComp-SIA / |
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#4: Sugar | ChemComp-GAL / |
#5: Sugar |
-Non-polymers , 1 types, 73 molecules
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.74 % / 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: 2.65→30 Å / Num. obs: 26200 / % possible obs: 100 % / Observed criterion σ(I): 4.4 / Redundancy: 10.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.6 |
-Processing
Software | Name: REFMAC / Version: 5.5.0088 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.65→30 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.882 / SU B: 23.432 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.433 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 49.265 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→30 Å
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