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Yorodumi- PDB-4bgy: H5 (VN1194) Influenza Virus Haemagglutinin in Complex with Avian ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bgy | |||||||||
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Title | H5 (VN1194) Influenza Virus Haemagglutinin in Complex with Avian Receptor Analogue 3'-SLN | |||||||||
Components | (HEMAGGLUTININ) x 2 | |||||||||
Keywords | VIRAL PROTEIN / N-GLYCOSYLATION / VIRUS RECEPTOR / BIRD FLU | |||||||||
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 VIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | |||||||||
Authors | Xiong, X. / Coombs, P. / Martin, S.R. / Liu, J. / Xiao, H. / McCauley, J.W. / Locher, K. / Walker, P.A. / Collins, P.J. / Kawaoka, Y. ...Xiong, X. / Coombs, P. / Martin, S.R. / Liu, J. / Xiao, H. / McCauley, J.W. / Locher, K. / Walker, P.A. / Collins, P.J. / Kawaoka, Y. / Skehel, J.J. / Gamblin, S.J. | |||||||||
Citation | Journal: Nature / Year: 2013 Title: Receptor Binding by a Ferret-Transmissible H5 Avian Influenza Virus. Authors: Xiong, X. / Coombs, P. / R Martin, S. / Liu, J. / Xiao, H. / Mccauley, J.W. / Locher, K. / Walker, P.A. / Collins, P.J. / Kawaoka, Y. / Skehel, J.J. / Gamblin, S.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bgy.cif.gz | 210.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bgy.ent.gz | 176.4 KB | Display | PDB format |
PDBx/mmJSON format | 4bgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/4bgy ftp://data.pdbj.org/pub/pdb/validation_reports/bg/4bgy | HTTPS FTP |
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-Related structure data
Related structure data | 4bgwC 4bgxC 4bgzC 4bh0C 4bh1C 4bh2C 4bh3C 4bh4C 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 on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 36950.766 Da / Num. of mol.: 1 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-340 Source method: isolated from a natural source Details: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC) Source: (natural) INFLUENZA VIRUS / Variant: A/VN/1194/04/NIBRG14 VACCINE STRAIN / Strain: A/VIETNAM/1194/2004 (H5N1) / 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 natural source Details: THE NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS AND CONTROL (NIBSC) Source: (natural) INFLUENZA VIRUS / Variant: A/VN/1194/04/NIBRG14 VACCINE STRAIN / Strain: A/VIETNAM/1194/2004 (H5N1) / References: UniProt: Q6DQ34 |
-Sugars , 2 types, 4 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine | |
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-Non-polymers , 2 types, 134 molecules
#5: Chemical | ChemComp-EPE / |
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#6: Water | ChemComp-HOH / |
-Details
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: 3.97 Å3/Da / Density % sol: 69.03 % / Description: NONE |
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Crystal grow | Details: 0.1 M HEPES PH 7.0, 0.05 M MGCL2, 28-30% PEG 550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 23, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→40.9 Å / Num. obs: 25658 / % possible obs: 100 % / Observed criterion σ(I): 3.1 / Redundancy: 9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.68→2.82 Å / Redundancy: 8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→40.94 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 20.203 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES WITH TLS ADDED. STRONG ELECTRON DENSITY FEATURE FOR THE NAG MOIETY OF AVIAN RECEPTOR IS OBSERVED BUT NOT VERY WELL DEFINED AND SO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES WITH TLS ADDED. STRONG ELECTRON DENSITY FEATURE FOR THE NAG MOIETY OF AVIAN RECEPTOR IS OBSERVED BUT NOT VERY WELL DEFINED AND SO THERE MAY BE OTHER CONFORMATIONS PRESENT AS WELL AS THE ONE WE HAVE BUILT.
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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: 75.629 Å2
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Refinement step | Cycle: LAST / Resolution: 2.68→40.94 Å
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