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Yorodumi- PDB-6icx: Crystal structure of H7 hemagglutinin mutant AH-AGPL (V186G) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6icx | ||||||
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Title | Crystal structure of H7 hemagglutinin mutant AH-AGPL (V186G) from the influenza virus A/Anhui/1/2013 (H7N9) | ||||||
Components |
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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 / 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 / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.399 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 | 6icx.cif.gz | 211.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6icx.ent.gz | 168.4 KB | Display | PDB format |
PDBx/mmJSON format | 6icx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/6icx ftp://data.pdbj.org/pub/pdb/validation_reports/ic/6icx | HTTPS FTP |
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-Related structure data
Related structure data | 6icwC 6icyC 6id2C 6id3C 6id5C 6id8C 6id9C 6idaC 6idbC 6iddC 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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Unit cell |
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-Components
#1: Protein | Mass: 34951.480 Da / Num. of mol.: 1 / Mutation: V177G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: R4NN21 | ||||||
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#2: Protein | Mass: 20442.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: R4NN21 | ||||||
#3: Sugar | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | Sequence reference R4NN21_9INFA was used according to author's suggestion. Author stated ...Sequence reference R4NN21_9INFA was used according to author's suggestion. Author stated hemagglutinin used in this studay, which was derived from AH1-H7N9 virus, was identical with R4NN21_9INFA. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.69 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M HEPES pH 7.0, 12% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.91847 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91847 Å / Relative weight: 1 |
Reflection | Resolution: 2.399→36.555 Å / Num. obs: 29523 / % possible obs: 99.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 21.69 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.633 / Num. unique obs: 2900 / Rsym value: 0.633 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KOL Resolution: 2.399→32.098 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.95 / 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: 2.399→32.098 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: -53.0135 Å / Origin y: 17.7424 Å / Origin z: 7.5925 Å
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Refinement TLS group | Selection details: all |