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Yorodumi- PDB-4bh0: H5 (tyTy) Influenza Virus Haemagglutinin in Complex with Human Re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bh0 | |||||||||
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Title | H5 (tyTy) 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 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 VIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | |||||||||
Authors | Xiong, X. / Coombs, P.J. / Martin, S.R. / Liu, J. / Xiao, H. / McCauley, J.W. / Locher, K. / Walker, P.A. / Collins, P.J. / Kawaoka, Y. ...Xiong, X. / Coombs, P.J. / 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.J. / 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 | 4bh0.cif.gz | 580.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bh0.ent.gz | 487.3 KB | Display | PDB format |
PDBx/mmJSON format | 4bh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bh0_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4bh0_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4bh0_validation.xml.gz | 57.9 KB | Display | |
Data in CIF | 4bh0_validation.cif.gz | 82 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/4bh0 ftp://data.pdbj.org/pub/pdb/validation_reports/bh/4bh0 | HTTPS FTP |
-Related structure data
Related structure data | 4bgwC 4bgxC 4bgyC 4bgzC 4bh1C 4bh2C 4bh3C 4bh4C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 36978.715 Da / Num. of mol.: 3 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA VIRUS / Strain: A/TURKEY/TURKEY/1/2005(H5N1) / 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 VIRUS / Strain: A/TURKEY/TURKEY/1/2005 (H5N1) / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q207Z6 |
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-Sugars , 3 types, 6 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: Polysaccharide | #5: Sugar | |
-Non-polymers , 2 types, 717 molecules
#6: Chemical | ChemComp-PO4 / #7: Water | ChemComp-HOH / | |
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-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: 3.11 Å3/Da / Density % sol: 60.46 % / 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: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→56.55 Å / Num. obs: 81446 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.36→2.49 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→56.61 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.896 / SU B: 14.973 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.246 / 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: 61.609 Å2
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Refinement step | Cycle: LAST / Resolution: 2.36→56.61 Å
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Refine LS restraints |
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