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- PDB-4cqx: H5 (tyTy) Del133/Ile155Thr Mutant Haemagglutinin in Complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cqx | |||||||||
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Title | H5 (tyTy) Del133/Ile155Thr Mutant Haemagglutinin in Complex with Human Receptor Analogue 6'SLN | |||||||||
![]() | (HAEMAGGLUTININ ...) x 2 | |||||||||
![]() | VIRAL PROTEIN / SIALIC ACID / GLYCOPROTEIN / VIRUS RECEPTOR / AVIAN FLU / SIALYLLACTOSAMINE / 3SLN / 3'SLN / 6SLN / 6'SLN / LSTA | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
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 | ![]() | 607.9 KB | Display | ![]() |
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PDB format | ![]() | 506.8 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 ![]() 4cqrC ![]() 4cqsC ![]() 4cquC ![]() 4cqvC ![]() 4cqwC ![]() 4cqyC ![]() 4cqzC ![]() 4cr0C ![]() 5ajmC ![]() 4bgzS 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: 1 / Refine code: 6
NCS ensembles :
NCS oper:
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Components
-HAEMAGGLUTININ ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 37010.672 Da / Num. of mol.: 3 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-342 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Variant: DEL133/ILE155THR MUTANT / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: ![]() ![]() #2: Protein | Mass: 19126.004 Da / Num. of mol.: 3 Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Variant: DEL133/ILE155THR MUTANT / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: ![]() ![]() |
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-Sugars , 2 types, 12 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 764 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-PO4 / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | MULTIBASIC |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | Details: BIS-TRIS PROPANE PH 7.5, 0.05 - 0.15 M K/NAPO4 (PH 7.0), 15-18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→87.73 Å / Num. obs: 90479 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BGZ Resolution: 2.3→101.17 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 15.315 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WITH TLS ADDED 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.219 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→101.17 Å
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Refine LS restraints |
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