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Yorodumi- PDB-4bsg: Crystal Structure of an H7N3 Avian Influenza Virus Haemagglutinin -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bsg | |||||||||
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Title | Crystal Structure of an H7N3 Avian Influenza Virus Haemagglutinin | |||||||||
Components | (HEMAGGLUTININ) x 2 | |||||||||
Keywords | VIRAL PROTEIN / H7N9 / H5N1 / FOWL PLAGUE VIRUS / SIALIC ACID / GLYCOPROTEIN / GLYCOSYLATION / VIRUS RECEPTOR / BIRD FLU / SIALYLLACTOSAMINE / 3SLN / 6SLN / LSTC / PANDEMIC | |||||||||
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 INFLUENZA A VIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Xiong, X. / Haire, L.F. / Martin, S.R. / Wharton, S.A. / Daniels, R.S. / Bennett, M.S. / McCauley, J.W. / Collins, P.J. / Walker, P.A. / Skehel, J.J. / Gamblin, S.J. | |||||||||
Citation | Journal: Nature / Year: 2013 Title: Receptor Binding by an H7N9 Influenza Virus from Humans Authors: Xiong, X. / Martin, S.R. / Haire, L.F. / Wharton, S.A. / Daniels, R.S. / Bennett, M.S. / Mccauley, J.W. / Collins, P.J. / Walker, P.A. / 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 | 4bsg.cif.gz | 214.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bsg.ent.gz | 174.5 KB | Display | PDB format |
PDBx/mmJSON format | 4bsg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bsg_validation.pdf.gz | 802.9 KB | Display | wwPDB validaton report |
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Full document | 4bsg_full_validation.pdf.gz | 810.4 KB | Display | |
Data in XML | 4bsg_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 4bsg_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/4bsg ftp://data.pdbj.org/pub/pdb/validation_reports/bs/4bsg | HTTPS FTP |
-Related structure data
Related structure data | 4bsaC 4bsbC 4bscC 4bsdC 4bseC 4bsfC 4bshC 4bsiC 1ti8S 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: 35087.539 Da / Num. of mol.: 1 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 19-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A (VIRUS A/TURKEY/ITALY/214845/2002 (H7N3)) Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q6GYW3 |
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#2: Protein | Mass: 20474.531 Da / Num. of mol.: 1 Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 340-516 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS (A/TURKEY/ITALY/214845/2002 (H7N3)) Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q6GYW3 |
-Sugars , 2 types, 3 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar |
-Non-polymers , 2 types, 309 molecules
#5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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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: 3.55 Å3/Da / Density % sol: 65 % / Description: NONE |
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Crystal grow | Temperature: 291 K Details: 291 K, 0.1 M PIPES PH 7.0, 2.2 M AMMONIUM SULFATE, 1% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→32.4 Å / Num. obs: 45139 / % possible obs: 99.8 % / Observed criterion σ(I): 2.17 / Redundancy: 6.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.49 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.17 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TI8 Resolution: 2.1→32.4 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.938 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.175 / 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: 54.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→32.4 Å
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Refine LS restraints |
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