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Yorodumi- PDB-6wex: Crystal Structure of Broadly Neutralizing Antibody 3I14-D93N Muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wex | |||||||||
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Title | Crystal Structure of Broadly Neutralizing Antibody 3I14-D93N Mutant Bound to the Influenza A H6 Hemagglutinin | |||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Antibody / Influenza / Hemagglutinin / Stem epitope / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
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 Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å | |||||||||
Authors | Harshbarger, W.D. / Lockbaum, G.J. / Deming, D.T. / Attatippaholkun, N. / Schiffer, C.A. / Marasco, W.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: Unique structural solution from a V H 3-30 antibody targeting the hemagglutinin stem of influenza A viruses. Authors: Harshbarger, W.D. / Deming, D. / Lockbaum, G.J. / Attatippaholkun, N. / Kamkaew, M. / Hou, S. / Somasundaran, M. / Wang, J.P. / Finberg, R.W. / Zhu, Q.K. / Schiffer, C.A. / Marasco, W.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wex.cif.gz | 235.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wex.ent.gz | 150.6 KB | Display | PDB format |
PDBx/mmJSON format | 6wex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wex_validation.pdf.gz | 484.5 KB | Display | wwPDB validaton report |
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Full document | 6wex_full_validation.pdf.gz | 510 KB | Display | |
Data in XML | 6wex_validation.xml.gz | 34.5 KB | Display | |
Data in CIF | 6wex_validation.cif.gz | 45.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/6wex ftp://data.pdbj.org/pub/pdb/validation_reports/we/6wex | HTTPS FTP |
-Related structure data
Related structure data | 6wezC 6wf0C 6wf1C 4xkdS 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: 36487.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0M3KL64 |
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#2: Protein | Mass: 25056.701 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X245 |
#3: Antibody | Mass: 25140.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) |
#4: Antibody | Mass: 22359.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) |
#5: Sugar | ChemComp-NAG / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M MIB Buffer (sodium malonate, imidazole, and boric acid in the molar ratios 2:3:3) pH 5.0, and 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.49→48.26 Å / Num. obs: 15294 / % possible obs: 99.3 % / Redundancy: 9.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.058 / Net I/σ(I): 9.89 |
Reflection shell | Resolution: 3.49→3.615 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 3.15 / Num. unique obs: 1421 / CC1/2: 0.86 / Rpim(I) all: 0.219 / Rrim(I) all: 0.686 / % possible all: 94.5 |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XKD Resolution: 3.49→48.26 Å / SU ML: 0.6936 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.513
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.49→48.26 Å
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Refine LS restraints |
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LS refinement shell |
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