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- PDB-4bsd: Human H7N9 Influenza Virus Haemagglutinin (with Asn-133 Glycosyla... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bsd | |||||||||
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Title | Human H7N9 Influenza Virus Haemagglutinin (with Asn-133 Glycosylation) in Complex with Avian Receptor Analogue 3'-SLN | |||||||||
![]() | (HEMAGGLUTININ) x 2 | |||||||||
![]() | VIRAL PROTEIN / FOWL PLAGUE VIRUS / SIALYLLACTOSAMINE | |||||||||
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 | INFLUENZA VIRUS A/ANHUI/1/2013 | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Xiong, X. / Haire, L.F. / Martin, S.R. / Wharton, S.A. / Daniels, R.S. / Bennett, M.S. / McCauley, J.W. / Collins, P.J. / Walker, P.A. / Skehel, J.J. / Gamblin, S.J. | |||||||||
![]() | ![]() Title: Receptor Binding by an H7N9 Influenza Virus from Humans Authors: Xiong, X. / Martin, S.R. / Haire, L.F. / Wharton, S.A. / Daniels, R.S. / Bennett, M.S. / Mccauley, J.W. / Collins, P.J. / Walker, P.A. / Skehel, J.J. / Gamblin, S.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 | ![]() | 216 KB | Display | ![]() |
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PDB format | ![]() | 175.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4bsaC ![]() 4bsbC ![]() 4bscC ![]() 4bseC ![]() 4bsfC ![]() 4bsgC ![]() 4bshC ![]() 4bsiC ![]() 1ti8S 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 on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 35037.613 Da / Num. of mol.: 1 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 19-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 20442.463 Da / Num. of mol.: 1 Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 340-516 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Sugars , 3 types, 6 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine |
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#4: 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 |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 154 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | GLOBAL INITIATIVE ON SHARING ALL INFLUENZA DATA (GISAID) V10L, A125T SUBSTITUTIONS ON GISAID- ...GLOBAL INITIATIVE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65 % / Description: NONE |
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Crystal grow | Temperature: 291 K Details: 291 K, 0.1 M PIPES PH 7.0, 2.2 M AMMONIUM SULFATE, 1% PEG 400 |
-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: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→59.56 Å / Num. obs: 30146 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.37 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TI8 Resolution: 2.4→59.56 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.901 / SU B: 20.172 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES 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: 60.762 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→59.56 Å
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Refine LS restraints |
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