+Open data
-Basic information
Entry | Database: PDB / ID: 8en2 | ||||||
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Title | Structure of GII.10 norovirus in complex with Nanobody 34 | ||||||
Components |
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Keywords | VIRAL PROTEIN / norovirus / nanobody | ||||||
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 / Capsid protein Function and homology information | ||||||
Biological species | Norovirus Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Kher, G. / Sabin, C. / Koromyslova, A. / Pancera, M. / 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 | 8en2.cif.gz | 185.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8en2.ent.gz | 144.5 KB | Display | PDB format |
PDBx/mmJSON format | 8en2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/8en2 ftp://data.pdbj.org/pub/pdb/validation_reports/en/8en2 | HTTPS FTP |
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-Related structure data
Related structure data | 8emyC 8emzC 8en0C 8en1C 8en3C 8en4C 8en5C 8en6C 3onuS 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: 34506.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q5F4T5 #2: Antibody | Mass: 13718.308 Da / Num. of mol.: 2 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: 2.35 Å3/Da / Density % sol: 47.6 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 1 M lithium chloride, 10% [w/v] PEG6000, and 0.1 M citric acid [pH 5] |
-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: 0.9762 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→80.528 Å / Num. obs: 75491 / % possible obs: 99.1 % / Redundancy: 7.065 % / Biso Wilson estimate: 31.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.08 / Χ2: 0.862 / Net I/σ(I): 16.48 / Num. measured all: 533312 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ONU Resolution: 1.85→51.4 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.19 / 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: 112.14 Å2 / Biso mean: 38.3858 Å2 / Biso min: 18.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→51.4 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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