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Yorodumi- PDB-5e34: Crystal structure of H5 hemagglutinin mutant (N224K, Q226L, N158D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5.0E+34 | |||||||||
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Title | Crystal structure of H5 hemagglutinin mutant (N224K, Q226L, N158D and L133a deletion) from the influenza virus A/chicken/Vietnam/NCVD-093/2008 (H5N1) with LSTa | |||||||||
Components | (Hemagglutinin) x 2 | |||||||||
Keywords | VIRAL PROTEIN / H5N1 influenza virus / hemagglutinin / receptor binding specificity / transmission / glycan complex | |||||||||
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 A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Zhu, X. / Wilson, I.A. | |||||||||
Citation | Journal: Cell Rep / Year: 2015 Title: Structural Basis for a Switch in Receptor Binding Specificity of Two H5N1 Hemagglutinin Mutants. Authors: Zhu, X. / Viswanathan, K. / Raman, R. / Yu, W. / Sasisekharan, R. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e34.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e34.ent.gz | 89.6 KB | Display | PDB format |
PDBx/mmJSON format | 5e34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e34_validation.pdf.gz | 804.5 KB | Display | wwPDB validaton report |
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Full document | 5e34_full_validation.pdf.gz | 811.4 KB | Display | |
Data in XML | 5e34_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 5e34_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/5e34 ftp://data.pdbj.org/pub/pdb/validation_reports/e3/5e34 | HTTPS FTP |
-Related structure data
Related structure data | 5e2yC 5e2zC 5e30C 5e32SC 5e35C S: Starting model for refinement 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
#1: Protein | Mass: 37663.824 Da / Num. of mol.: 1 / Fragment: UNP residues 17-346 / Mutation: N224K, Q226L, N158D and L133a deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/chicken/Vietnam/NCVD-093/2008(H5N1)) Strain: A/chicken/Vietnam/NCVD-093/2008(H5N1) / Gene: HA / Plasmid: PFASTBAC-HT / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C4P282 | ||
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#2: Protein | Mass: 20793.016 Da / Num. of mol.: 1 / Fragment: UNP residues 347-521 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/chicken/Vietnam/NCVD-093/2008(H5N1) / Gene: HA / Plasmid: BACULOVIRUS / Details (production host): PFASTBAC-HT / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C4P282 | ||
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Sugar | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.7 Å3/Da / Density % sol: 78.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M ammonium acetate, 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03314 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03314 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 34678 / % possible obs: 98.1 % / Redundancy: 7.5 % / Rsym value: 0.16 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.7→2.76 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.71 / % possible all: 79.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 5.0E+32 / Resolution: 2.7→46.696 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→46.696 Å
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Refine LS restraints |
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LS refinement shell |
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