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- PDB-8emz: Structure of GII.17 norovirus in complex with Nanobody 2 -

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Basic information

Entry
Database: PDB / ID: 8emz
TitleStructure of GII.17 norovirus in complex with Nanobody 2
Components
  • GII.17 P domain
  • Nanobody 2Single-domain antibody
KeywordsVIRAL PROTEIN / norovirus / Nanobody / inhibitor
Function / homologyCalicivirus 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 speciesNorovirus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKher, G. / Sabin, C. / Pancera, M. / Koromyslova, A. / Hansman, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: 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
DepositionSep 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GII.17 P domain
B: Nanobody 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,16418
Polymers48,1702
Non-polymers99316
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.961, 90.545, 59.397
Angle α, β, γ (deg.)90.000, 116.290, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-762-

HOH

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Components

#1: Protein GII.17 P domain


Mass: 34041.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S1Z370
#2: Antibody Nanobody 2 / Single-domain antibody


Mass: 14128.556 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M bicine [pH 9] and 30% [w/v] PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.4→117.53 Å / Num. obs: 85355 / % possible obs: 98.5 % / Redundancy: 7.009 % / Biso Wilson estimate: 20.02 Å2 / CC1/2: 1 / Net I/σ(I): 19.1
Reflection shellResolution: 2.97→4.19 Å / Redundancy: 7.015 % / Num. unique obs: 2485 / CC1/2: 1

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5f4o

5f4o


Resolution: 1.4→48.85 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 1999 2.34 %
Rwork0.1953 83328 -
obs0.1959 85327 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.42 Å2 / Biso mean: 28.5252 Å2 / Biso min: 12.75 Å2
Refinement stepCycle: final / Resolution: 1.4→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 136 286 3822
Biso mean--42.75 32.99 -
Num. residues----433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.440.3521400.3035841598198
1.44-1.470.27331420.28075919606198
1.47-1.520.31311400.27065888602898
1.52-1.570.29831430.25695900604398
1.57-1.620.3051410.25245900604198
1.62-1.690.27981430.23825952609599
1.69-1.760.24631430.22495975611899
1.76-1.860.23041440.21766005614999
1.86-1.970.23251430.21255928607199
1.97-2.130.23441420.20175949609199
2.13-2.340.24741430.20145955609899
2.34-2.680.21581450.203560396184100
2.68-3.370.20641440.188260266170100
3.38-48.850.18091460.15666051619799

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