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Yorodumi- PDB-6bkm: Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza viru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bkm | ||||||||||||
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Title | Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin E190D mutant apo form | ||||||||||||
Components | (Hemagglutinin) x 2 | ||||||||||||
Keywords | VIRAL PROTEIN / Influenza / Hemagglutinin / Receptor | ||||||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / membrane Similarity search - Function | ||||||||||||
Biological species | Influenza A virus | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||
Authors | Wu, N.C. / Wilson, I.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2018 Title: A complex epistatic network limits the mutational reversibility in the influenza hemagglutinin receptor-binding site. Authors: Wu, N.C. / Thompson, A.J. / Xie, J. / Lin, C.W. / Nycholat, C.M. / Zhu, X. / Lerner, R.A. / Paulson, J.C. / 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 | 6bkm.cif.gz | 605.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bkm.ent.gz | 500.2 KB | Display | PDB format |
PDBx/mmJSON format | 6bkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/6bkm ftp://data.pdbj.org/pub/pdb/validation_reports/bk/6bkm | HTTPS FTP |
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-Related structure data
Related structure data | 6bknC 6bkoC 6bkpC 6bkqC 6bkrC 6bksC 6bktC 4fnkS 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 35492.922 Da / Num. of mol.: 3 / Mutation: E190D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2) Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7 #2: Protein | Mass: 20041.131 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Northern Territory/60/1968 H3N2) Strain: A/Northern Territory/60/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03436 |
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-Sugars , 5 types, 12 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 699 molecules
#8: Chemical | ChemComp-TAM / |
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#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M sodium cacodylate pH 6.5, 6% PEG 8000, and 39% 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 96961 / % possible obs: 99.4 % / Redundancy: 4.5 % / CC1/2: 1 / Rpim(I) all: 0.05 / Rsym value: 0.1 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9442 / CC1/2: 0.71 / Rpim(I) all: 0.44 / Rsym value: 0.71 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FNK Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 11.397 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.173 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.69 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→50 Å
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Refine LS restraints |
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