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Yorodumi- PDB-5e2z: Crystal structure of H5 hemagglutinin Q226L mutant from the influ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e2z | |||||||||
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Title | Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/duck/Egypt/10185SS/2010 (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: 2.624 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 | 5e2z.cif.gz | 317.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e2z.ent.gz | 256.2 KB | Display | PDB format |
PDBx/mmJSON format | 5e2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/5e2z ftp://data.pdbj.org/pub/pdb/validation_reports/e2/5e2z | HTTPS FTP |
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-Related structure data
Related structure data | 5e2ySC 5e30C 5e32C 5e34C 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
-Protein , 2 types, 6 molecules CAEDBF
#1: Protein | Mass: 37701.578 Da / Num. of mol.: 3 / Fragment: UNP residues 17-345 / Mutation: Q226L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/duck/Egypt/10185SS/2010(H5N1)) Strain: A/duck/Egypt/10185SS/2010(H5N1) / Gene: HA / Plasmid: PFASTBAC-HT / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): Hi5 / References: UniProt: G8IPF0 #2: Protein | Mass: 20822.039 Da / Num. of mol.: 3 / Fragment: UNP residues 347-520 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/duck/Egypt/10185SS/2010(H5N1) / Gene: HA / Plasmid: BACULOVIRUS / Details (production host): PFASTBAC-HT / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): Hi5 / References: UniProt: G8IPF0 |
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-Sugars , 5 types, 9 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: 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 #7: Sugar | |
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-Non-polymers , 1 types, 167 molecules
#8: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 61.66 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.085 M Tris, pH 8.5, 10% (v/v) glycerol, 0.17% (w/v) sodium acetate, 21% (w/v) PEG4000. |
-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: 2.6→50 Å / Num. obs: 57187 / % possible obs: 89.4 % / Redundancy: 3.3 % / Rsym value: 0.11 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 3 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.6 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5E2Y Resolution: 2.624→50 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.08 / 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: 2.624→50 Å
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Refine LS restraints |
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LS refinement shell |
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