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Yorodumi- PDB-4cr0: Crystal Structure of H5 (VN1194) Asn186Lys/Gly143Arg Mutant Haema... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cr0 | ||||||
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Title | Crystal Structure of H5 (VN1194) Asn186Lys/Gly143Arg 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 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 / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Collins, P.J. / Vachieri, S.G. / Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Walker, P.A. / Lin, Y.P. / McCauley, J.W. ...Collins, P.J. / Vachieri, S.G. / Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / 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 | 4cr0.cif.gz | 208.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cr0.ent.gz | 167.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cr0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/4cr0 ftp://data.pdbj.org/pub/pdb/validation_reports/cr/4cr0 | HTTPS FTP |
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-Related structure data
Related structure data | 4cqpC 4cqqC 4cqrC 4cqsC 4cquC 4cqvC 4cqwC 4cqxC 4cqyC 4cqzC 5ajmC 4bgwS 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: 37065.984 Da / Num. of mol.: 1 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-340 Mutation: N168K,G143R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Gallus gallus (chicken) / References: UniProt: Q6DQ34 | ||||
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#2: Protein | Mass: 19087.953 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 / Gene: HA / Production host: Gallus gallus (chicken) / References: UniProt: Q6DQ34 | ||||
#3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | Sequence details | MULTIBASIC | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | Details: 0.1 M MOPS PH 7.0, 12% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / 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: 2.65→67.51 Å / Num. obs: 20820 / % possible obs: 99.1 % / Observed criterion σ(I): 2.6 / Redundancy: 5.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.6 / % possible all: 99.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BGW Resolution: 2.65→105.21 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.875 / SU B: 26.777 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 0.64 / ESU R Free: 0.32 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.967 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→105.21 Å
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Refine LS restraints |
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