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Yorodumi- PDB-4bgx: H5 (VN1194) Influenza Virus Haemagglutinin in Complex with Human ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bgx | |||||||||
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Title | H5 (VN1194) Influenza Virus Haemagglutinin in Complex with Human Receptor Analogue 6'-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: 2.48 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 | 4bgx.cif.gz | 218.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bgx.ent.gz | 176.3 KB | Display | PDB format |
PDBx/mmJSON format | 4bgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/4bgx ftp://data.pdbj.org/pub/pdb/validation_reports/bg/4bgx | HTTPS FTP |
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-Related structure data
Related structure data | 4bgwC 4bgyC 4bgzC 4bh0C 4bh1C 4bh2C 4bh3C 4bh4C 2ibxS 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 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 | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar |
-Non-polymers , 2 types, 212 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: 3.98 Å3/Da / Density % sol: 69.07 % / 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: 2.48→37.15 Å / Num. obs: 32249 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 9.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.48→2.61 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IBX Resolution: 2.48→37.18 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 13.959 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.792 Å2
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Refinement step | Cycle: LAST / Resolution: 2.48→37.18 Å
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Refine LS restraints |
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