+Open data
-Basic information
Entry | Database: PDB / ID: 8emy | ||||||
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Title | Structure of GII.4 norovirus in complex with Nanobody 82 | ||||||
Components |
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Keywords | VIRAL PROTEIN / norovirus / Nanobody / inhibitor | ||||||
Function / homology | Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / VP1 Function and homology information | ||||||
Biological species | Norovirus Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kher, G. / Sabin, C. / Pancera, M. / Koromyslova, A. / Hansman, G. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Virol. / Year: 2023 Title: Direct Blockade of the Norovirus Histo-Blood Group Antigen Binding Pocket by Nanobodies. Authors: Kher, G. / Sabin, C. / Lun, J.H. / Devant, J.M. / Ruoff, K. / Koromyslova, A.D. / von Itzstein, M. / Pancera, M. / Hansman, G.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8emy.cif.gz | 547.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8emy.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8emy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/8emy ftp://data.pdbj.org/pub/pdb/validation_reports/em/8emy | HTTPS FTP |
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-Related structure data
Related structure data | 8emzC 8en0C 8en1C 8en2C 8en3C 8en4C 8en5C 8en6C 4oosS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34074.988 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus / Production host: Escherichia coli (E. coli) / References: UniProt: K4LM89 #2: Antibody | Mass: 13355.741 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.17 Å3/Da / Density % sol: 61.16 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 5% [w/v] PEG 6000 and 0.1M HEPES [pH 7.0] |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→117.53 Å / Num. obs: 380256 / % possible obs: 96.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 21.7 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.022 / Rrim(I) all: 0.046 / Net I/σ(I): 19.1 / Num. measured all: 1649444 / Scaling rejects: 38616 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4oos Resolution: 1.7→61.39 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.95 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.85 Å2 / Biso mean: 26.3757 Å2 / Biso min: 12.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→61.39 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27
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