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Yorodumi- PDB-4cqv: Crystal structure of H5 (tyTy) Del133/Ile155Thr Mutant Haemagglutinin -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cqv | ||||||
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Title | Crystal structure of H5 (tyTy) Del133/Ile155Thr Mutant Haemagglutinin | ||||||
Components |
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Keywords | VIRAL PROTEIN / SIALIC ACID / GLYCOPROTEIN / VIRUS RECEPTOR / AVIAN FLU / SIALYLLACTOSAMINE / 3SLN / 3'SLN / 6SLN / 6'SLN / LSTA | ||||||
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 | INFLUENZA A VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å | ||||||
Authors | Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / McCauley, J.W. ...Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / McCauley, J.W. / Gamblin, S.J. / Skehel, J.J. | ||||||
Citation | Journal: Virology / Year: 2014 Title: Enhanced Human Receptor Binding by H5 Haemagglutinins. Authors: Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / Mccauley, J.W. / Gamblin, S.J. / Skehel, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cqv.cif.gz | 599.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cqv.ent.gz | 504.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cqv_validation.pdf.gz | 505.7 KB | Display | wwPDB validaton report |
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Full document | 4cqv_full_validation.pdf.gz | 519.4 KB | Display | |
Data in XML | 4cqv_validation.xml.gz | 53.2 KB | Display | |
Data in CIF | 4cqv_validation.cif.gz | 72.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/4cqv ftp://data.pdbj.org/pub/pdb/validation_reports/cq/4cqv | HTTPS FTP |
-Related structure data
Related structure data | 4cqpC 4cqqC 4cqrC 4cqsC 4cquC 4cqwC 4cqxC 4cqyC 4cqzC 4cr0C 5ajmC 4bgzS C: citing same article (ref.) S: Starting model for refinement |
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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: 37010.672 Da / Num. of mol.: 3 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 (A/TURKEY/TURKEY/1/2005(H5N1)) Variant: DEL133/ILE155THR MUTANT / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q207Z6 #2: Protein | Mass: 19126.004 Da / Num. of mol.: 3 Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS (A/TURKEY/TURKEY/1/2005(H5N1)) Variant: DEL133/ILE155THR MUTANT / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q207Z6 #3: Sugar | ChemComp-NAG / #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | Sequence details | MULTIBASIC | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | Details: BIS-TRIS PROPANE PH 7.5, 0.05 - 0.15 M K/NAPO4 (PH 7.0), 15-18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.86→70.03 Å / Num. obs: 46268 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.86→3.01 Å / Redundancy: 3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2 / % possible all: 99 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BGZ Resolution: 2.86→70.13 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 32.202 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.448 Å2
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Refinement step | Cycle: LAST / Resolution: 2.86→70.13 Å
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Refine LS restraints |
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