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- PDB-5vu4: 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: 5vu4 | |||||||||
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Title | Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin G225Q/L226A mutant in complex with 6'-SLN | |||||||||
![]() | (Hemagglutinin ...) x 2 | |||||||||
![]() | VIRAL PROTEIN / Influenza A virus / hemagglutinin / mutant / receptor binding | |||||||||
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: Diversity of Functionally Permissive Sequences in the Receptor-Binding Site of Influenza Hemagglutinin. Authors: Wu, N.C. / Xie, J. / Zheng, T. / Nycholat, C.M. / Grande, G. / Paulson, J.C. / Lerner, R.A. / 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 | ![]() | 611.6 KB | Display | ![]() |
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PDB format | ![]() | 507.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
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Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 59.3 KB | Display | |
Data in CIF | ![]() | 85 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vtqC ![]() 5vtrC ![]() 5vtuC ![]() 5vtvC ![]() 5vtwC ![]() 5vtxC ![]() 5vtyC ![]() 5vtzC ![]() 4fnkS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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
-Hemagglutinin ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 35535.945 Da / Num. of mol.: 3 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/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: ![]() |
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-Sugars , 7 types, 13 molecules 


#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 | ||||||||||
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#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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 #7: 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 #8: Sugar | ChemComp-NAG / #9: Sugar | |
-Non-polymers , 1 types, 685 molecules 
#10: Water | ChemComp-HOH / |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.51 % |
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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, 5% PEG 8000, and 38% 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: Oct 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0331 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 91825 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 1 / Rpim(I) all: 0.03 / Rsym value: 0.08 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.25→2.32 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 8243 / Rpim(I) all: 0.27 / Rsym value: 0.6 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FNK Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 10.835 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.181 / 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: 55.453 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→50 Å
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Refine LS restraints |
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