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Yorodumi- PDB-6n8d: Crystal structure of GII.4 2002 norovirus P domain in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n8d | ||||||
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Title | Crystal structure of GII.4 2002 norovirus P domain in complex with neutralizing human antibody A1431 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Norovirus / human antibody / Fab / complex / neutralizing | ||||||
Function / homology | Function and homology information Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Norovirus Hu/GII.4/Farmington Hills/2004/USA Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Changela, A. / Verardi, R. / Kwong, P.D. | ||||||
Citation | Journal: Immunity / Year: 2019 Title: Sera Antibody Repertoire Analyses Reveal Mechanisms of Broad and Pandemic Strain Neutralizing Responses after Human Norovirus Vaccination. Authors: Lindesmith, L.C. / McDaniel, J.R. / Changela, A. / Verardi, R. / Kerr, S.A. / Costantini, V. / Brewer-Jensen, P.D. / Mallory, M.L. / Voss, W.N. / Boutz, D.R. / Blazeck, J.J. / Ippolito, G.C. ...Authors: Lindesmith, L.C. / McDaniel, J.R. / Changela, A. / Verardi, R. / Kerr, S.A. / Costantini, V. / Brewer-Jensen, P.D. / Mallory, M.L. / Voss, W.N. / Boutz, D.R. / Blazeck, J.J. / Ippolito, G.C. / Vinje, J. / Kwong, P.D. / Georgiou, G. / Baric, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n8d.cif.gz | 576 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n8d.ent.gz | 476.9 KB | Display | PDB format |
PDBx/mmJSON format | 6n8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/6n8d ftp://data.pdbj.org/pub/pdb/validation_reports/n8/6n8d | HTTPS FTP |
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-Related structure data
Related structure data | 6n81C 3eyqS 4oovS C: citing same article (ref.) S: Starting model for refinement |
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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: 33940.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus Hu/GII.4/Farmington Hills/2004/USA Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4I4P2 #2: Antibody | Mass: 23520.264 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: Antibody | Mass: 24926.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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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: 3.58 Å3/Da / Density % sol: 65.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 8000, 0.1M CHES, pH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 39673 / % possible obs: 94.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2068 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OOV, 3EYQ Resolution: 3.1→41.622 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→41.622 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 |
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