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Yorodumi- PDB-6idd: Crystal structure of H7 hemagglutinin mutant SH1-AVPL ( S138A, G1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6idd | ||||||
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Title | Crystal structure of H7 hemagglutinin mutant SH1-AVPL ( S138A, G186V, T221P, Q226L) from the influenza virus A/Shanghai/1/2013 (H7N9) | ||||||
Components | Hemagglutinin | ||||||
Keywords | VIRAL PROTEIN / influenza virus / H7N9 / Hemagglutinin | ||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.383 Å | ||||||
Authors | Gao, G.F. / Xu, Y. / Qi, J.X. | ||||||
Citation | Journal: Cell Rep / Year: 2019 Title: Avian-to-Human Receptor-Binding Adaptation of Avian H7N9 Influenza Virus Hemagglutinin. Authors: Xu, Y. / Peng, R. / Zhang, W. / Qi, J. / Song, H. / Liu, S. / Wang, H. / Wang, M. / Xiao, H. / Fu, L. / Fan, Z. / Bi, Y. / Yan, J. / Shi, Y. / 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 | 6idd.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6idd.ent.gz | 950.2 KB | Display | PDB format |
PDBx/mmJSON format | 6idd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/6idd ftp://data.pdbj.org/pub/pdb/validation_reports/id/6idd | HTTPS FTP |
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-Related structure data
Related structure data | 6icwC 6icxC 6icyC 6id2C 6id3C 6id5C 6id8C 6id9C 6idaC 6idbC 6idzC 4kolS S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 55457.949 Da / Num. of mol.: 6 / Mutation: S165N,N267D,H274Y,N392T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Shanghai/MH01/2013(H7N9)) Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A088BEK2 #2: Sugar | ChemComp-NAG / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M Sodium HEPES pH 7.5, 14% w/v PEG 4000, 7% v/v 2-Propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97922 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→50 Å / Num. obs: 150579 / % possible obs: 98.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 11.37 |
Reflection shell | Resolution: 2.38→2.47 Å / Rmerge(I) obs: 0.864 / Num. unique obs: 13391 / Rsym value: 0.864 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KOL Resolution: 2.383→40.549 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.383→40.549 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 148.6315 Å / Origin y: 6.2791 Å / Origin z: 133.4352 Å
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Refinement TLS group | Selection details: all |