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Yorodumi- PDB-4kom: The structure of hemagglutinin from avian-origin H7N9 influenza v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kom | |||||||||
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Title | The structure of hemagglutinin from avian-origin H7N9 influenza virus in complex with avian receptor analog 3'SLNLN (NeuAcα2-3Galβ1-4GlcNAcβ1-3Galβ1-4Glc) | |||||||||
Components |
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Keywords | VIRAL PROTEIN / homotrimer / virus attachment and membrane fusion | |||||||||
Function / homology | Function and homology information 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 Similarity search - Function | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 Å | |||||||||
Authors | Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Song, H. / Wu, Y. / Gao, F. / Zhang, Y. / Fan, Z. / Gong, W. ...Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Song, H. / Wu, Y. / Gao, F. / Zhang, Y. / Fan, Z. / Gong, W. / Wang, D. / Shu, Y. / Wang, Y. / Yan, J. / Gao, G.F. | |||||||||
Citation | Journal: Science / Year: 2013 Title: Structures and receptor binding of hemagglutinins from human-infecting H7N9 influenza viruses. Authors: Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Wu, Y. / Song, H. / Gao, F. / Bi, Y. / Zhang, Y. / Fan, Z. / Qin, C. / Sun, H. / Liu, J. / Haywood, J. / Liu, W. / Gong, W. / Wang, D. / Shu, Y. / ...Authors: Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Wu, Y. / Song, H. / Gao, F. / Bi, Y. / Zhang, Y. / Fan, Z. / Qin, C. / Sun, H. / Liu, J. / Haywood, J. / Liu, W. / Gong, W. / Wang, D. / Shu, Y. / Wang, Y. / Yan, J. / Gao, G.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kom.cif.gz | 205.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kom.ent.gz | 169.5 KB | Display | PDB format |
PDBx/mmJSON format | 4kom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/4kom ftp://data.pdbj.org/pub/pdb/validation_reports/ko/4kom | HTTPS FTP |
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-Related structure data
Related structure data | 4kolC 4konC 4lcxC 4lkgC 4lkhC 4lkiC 4lkjC 4lkkC C: citing same article (ref.) |
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Similar structure data |
-Links
-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
#1: Protein | Mass: 34195.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Anhui/1/2013 (H7N9) / Gene: HA / Plasmid: pFastbac1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: V5IRU4*PLUS | ||
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#2: Protein | Mass: 19490.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Anhui/1/2013 (H7N9) / Gene: HA / Plasmid: pFastbac1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: V5IRU3*PLUS | ||
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source | ||
#4: Sugar | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 16% w/v PEG 3350, 0.2 M lithium sulfate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 24232 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.604→39.075 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 26.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.228 Å2 / ksol: 0.283 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.604→39.075 Å
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Refine LS restraints |
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LS refinement shell |
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