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- PDB-8en2: Structure of GII.10 norovirus in complex with Nanobody 34 -

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Basic information

Entry
Database: PDB / ID: 8en2
TitleStructure of GII.10 norovirus in complex with Nanobody 34
Components
  • GII.10 P domain
  • Nanobody 34
KeywordsVIRAL PROTEIN / norovirus / nanobody
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 / Capsid protein
Function and homology information
Biological speciesNorovirus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKher, G. / Sabin, C. / Koromyslova, A. / Pancera, M. / 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.10 P domain
C: Nanobody 34
B: GII.10 P domain
D: Nanobody 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5125
Polymers96,4504
Non-polymers621
Water5,296294
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)66.781, 80.528, 84.206
Angle α, β, γ (deg.)90.000, 90.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GII.10 P domain


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 Nanobody 34


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 / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 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]

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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 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.967.0151.1071.738480812272120890.7071.19598.5
1.96-2.17.0620.6113.158072811504114320.8790.6699.4
2.1-2.277.1290.3635.337605410730106690.9520.39199.4
2.27-2.487.0990.2218.5269686993098160.9810.23898.9
2.48-2.777.0350.13812.9862336894388610.9910.14999.1
2.77-3.26.9650.07422.9654873790978780.9980.0899.6
3.2-3.927.1790.04141.7747842669366640.9990.04499.6
3.92-5.547.0230.02856.6536401524351830.9990.0398.9
5.54-80.5287.10.02661.76205842938289910.02898.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONU

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
RfactorNum. reflection% reflection
Rfree0.2344 1996 2.65 %
Rwork0.2084 73447 -
obs0.2091 75443 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.14 Å2 / Biso mean: 38.3858 Å2 / Biso min: 18.44 Å2
Refinement stepCycle: final / Resolution: 1.85→51.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6758 0 10 294 7062
Biso mean--20 33.68 -
Num. residues----876
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 (%)
1.85-1.90.3941420.34395136527898
1.9-1.950.33871430.29445249539299
1.95-2.010.29331570.27625190534799
2.01-2.070.2771280.2575237536599
2.07-2.140.28941560.250452285384100
2.14-2.230.29541340.25085285541999
2.23-2.330.23651440.235211535599
2.33-2.450.29481410.23715223536499
2.45-2.610.2481380.23395215535399
2.61-2.810.26021450.23975251539699
2.81-3.090.22731440.228452705414100
3.09-3.540.23641470.208752995446100
3.54-4.460.18131440.16735309545399
4.46-51.40.19251330.15685344547799

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