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Yorodumi- PDB-6d0u: Crystal structure of C05 V110P/A117E mutant bound to H3 influenza... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d0u | ||||||
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Title | Crystal structure of C05 V110P/A117E mutant bound to H3 influenza hemagglutinin, HA1 subunit | ||||||
Components |
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Keywords | ANTIVIRAL PROTEIN / Computational design / Antibody / Influenza / 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 / 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 / membrane Similarity search - Function | ||||||
Biological species | Influenza A virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Wu, N.C. / Wilson, I.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019 Title: Multistate design of influenza antibodies improves affinity and breadth against seasonal viruses. Authors: Sevy, A.M. / Wu, N.C. / Gilchuk, I.M. / Parrish, E.H. / Burger, S. / Yousif, D. / Nagel, M.B.M. / Schey, K.L. / Wilson, I.A. / Crowe Jr., J.E. / Meiler, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d0u.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6d0u.ent.gz | 923.5 KB | Display | PDB format |
PDBx/mmJSON format | 6d0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/6d0u ftp://data.pdbj.org/pub/pdb/validation_reports/d0/6d0u | HTTPS FTP |
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-Related structure data
Related structure data | 4fp8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 30391.104 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7 #2: Antibody | Mass: 26376.312 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) #3: Antibody | Mass: 23367.018 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) #4: Sugar | |
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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: 3.39 Å3/Da / Density % sol: 63.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M sodium citrate pH 5.5 and 20% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2017 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 3.25→50 Å / Num. obs: 64646 / % possible obs: 96 % / Redundancy: 4.3 % / Biso Wilson estimate: 63 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.09 / Rsym value: 0.16 / Net I/σ(I): 8.9 | |||||||||||||||
Reflection shell | Resolution: 3.25→3.35 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5630 / CC1/2: 0.5 / Rpim(I) all: 0.43 / Rsym value: 0.78 / % possible all: 93 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 4FP8 Resolution: 3.25→50 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.885 / SU B: 37.037 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R Free: 0.114 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 116.503 Å2
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Refinement step | Cycle: 1 / Resolution: 3.25→50 Å
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Refine LS restraints |
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