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- PDB-4cqr: H5 (VN1194) Ser227Asn/Gln196Arg Mutant Haemagglutinin in Complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cqr | |||||||||
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Title | H5 (VN1194) Ser227Asn/Gln196Arg Mutant Haemagglutinin in Complex with Human Receptor Analogue 6'SLN | |||||||||
![]() | (Hemagglutinin ...![]() | |||||||||
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Function / homology | ![]() 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 / ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / McCauley, J.W. ...Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / McCauley, J.W. / Gamblin, S.J. / Skehel, J.J. | |||||||||
![]() | ![]() Title: Enhanced Human Receptor Binding by H5 Haemagglutinins. Authors: Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / Mccauley, J.W. / Gamblin, S.J. / Skehel, J.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.4 KB | Display | ![]() |
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PDB format | ![]() | 176 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4cqpC ![]() 4cqqC ![]() 4cqsC ![]() 4cquC ![]() 4cqvC ![]() 4cqwC ![]() 4cqxC ![]() 4cqyC ![]() 4cqzC ![]() 4cr0C ![]() 5ajmC ![]() 4bgwS 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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1 | ![]()
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Unit cell |
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Components
-Hemagglutinin ... , 2 types, 2 molecules AB
#1: Protein | Mass: 37006.852 Da / Num. of mol.: 1 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-342 Mutation: S227N/Q196R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 19097.990 Da / Num. of mol.: 1 Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
-Sugars , 5 types, 6 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | 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 | beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-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 |
#5: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose![]() Source method: isolated from a genetically manipulated source |
#6: 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 |
#7: Sugar | ![]() |
-Non-polymers , 2 types, 73 molecules ![](data/chem/img/MPO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | ChemComp-MPO / ![]() |
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#9: Water | ChemComp-HOH / ![]() |
-Details
Sequence details | MULTIBASIC |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67 % / Description: NONE |
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Crystal grow![]() | Details: 0.1 M HEPES/MOPS PH 7.0, 0.05 M MGCL2, 28-30% PEG 550 MME, SEEDED WITH CRUSHED WILD-TYPE VN1194 HA CRYSTALS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.45→40.81 Å / Num. obs: 33089 / % possible obs: 99.5 % / Observed criterion σ(I): 2.1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4BGW Resolution: 2.45→150.45 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 18.108 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.757 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→150.45 Å
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Refine LS restraints |
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