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- PDB-6bkm: Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza viru... -
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Open data
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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 | ||||||||||||
![]() | (Hemagglutinin) x 2 | ||||||||||||
![]() | VIRAL PROTEIN / Influenza / Hemagglutinin / Receptor | ||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Wu, N.C. / Wilson, I.A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 605.2 KB | Display | ![]() |
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PDB format | ![]() | 500.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 59.4 KB | Display | |
Data in CIF | ![]() | 84.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bknC ![]() 6bkoC ![]() 6bkpC ![]() 6bkqC ![]() 6bkrC ![]() 6bksC ![]() 6bktC ![]() 4fnkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
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.) ![]() Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: ![]() #2: Protein | Mass: 20041.131 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Northern Territory/60/1968 H3N2 / Gene: HA / Production host: ![]() |
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-Sugars , 5 types, 12 molecules ![](data/chem/img/NAG.gif)
#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 ![](data/chem/img/TAM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | ChemComp-TAM / |
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#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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