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Yorodumi- PDB-8gv4: A human broadly neutralizing influenza A hemagglutinin stem-speci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gv4 | ||||||
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Title | A human broadly neutralizing influenza A hemagglutinin stem-specific antibody PN-SIA28 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Influenza / hemagglutinin / antibody / broadly neutralizing | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Chen, Y. / Song, H. / Qi, J. / Gao, G.F. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for a human broadly neutralizing influenza A hemagglutinin stem-specific antibody including H17/18 subtypes. Authors: Chen, Y. / Wang, F. / Yin, L. / Jiang, H. / Lu, X. / Bi, Y. / Zhang, W. / Shi, Y. / Burioni, R. / Tong, Z. / Song, H. / Qi, 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 | 8gv4.cif.gz | 382 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gv4.ent.gz | 277.8 KB | Display | PDB format |
PDBx/mmJSON format | 8gv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/8gv4 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/8gv4 | HTTPS FTP |
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-Related structure data
Related structure data | 7wvdC 7wvgC 7wviC 8gv5C 8gv6C 8gv7C 5gjsS S: Starting model for refinement C: citing same article (ref.) |
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-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: Antibody | Mass: 24400.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human) #2: Antibody | Mass: 24046.721 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Water | ChemComp-HOH / | |
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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: 2.73 Å3/Da / Density % sol: 54.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH7.0, 12% PEG 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: 1.03906 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03906 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 36196 / % possible obs: 97.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 31.05 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 7.9 / Num. unique obs: 7086 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GJS Resolution: 2.5→42.14 Å / SU ML: 0.2392 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.7678 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→42.14 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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