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- PDB-8en0: Structure of GII.17 norovirus in complex with Nanobody 7 -

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Basic information

Entry
Database: PDB / ID: 8en0
TitleStructure of GII.17 norovirus in complex with Nanobody 7
Components
  • Capsid protein VP1
  • Nanobody 7
KeywordsVIRAL PROTEIN / norovirus / Nanobody / inhibitor
Function / homology
Function and homology information


virion component / host cell cytoplasm
Similarity search - Function
Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesVicugna pacos (alpaca)
Norovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Nanobody 7
A: Capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)48,9602
Polymers48,9602
Non-polymers00
Water37821
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)74.820, 85.459, 223.853
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Antibody Nanobody 7


Mass: 14645.071 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)
#2: Protein Capsid protein VP1 / Major capsid protein / Major viral capsid protein / VP1 / VP1 capsid protein / Viral protein 1


Mass: 34315.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Gene: VP1, ORF2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S1Z370
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.65 Å3/Da / Density % sol: 66.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.8 M ammonium sulfate and 0.1M citric acid [pH 4]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / 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: 2.99→111.926 Å / Num. obs: 14280 / % possible obs: 95.5 % / Redundancy: 13.219 % / Biso Wilson estimate: 74.27 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.286 / Rrim(I) all: 0.298 / Χ2: 0.722 / Net I/σ(I): 9.1 / Num. measured all: 188769
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
2.99-3.1713.341.8591.3130868236323140.5661.93497.9
3.17-3.3913.6721.1562.2730503223122310.8091.201100
3.39-3.6613.3460.4953.3624450208718320.9940.51887.8
3.66-4.0112.3320.2786.7119325193415670.9940.29381
4.01-4.4813.4170.22310.9823546175717550.9910.23299.9
4.48-5.1713.180.16814.7220521155715570.9930.174100
5.17-6.3313.4630.1714.3918041134113400.9930.17799.9
6.33-8.9413.1440.10921.1213854105410540.9970.113100
8.94-111.92612.160.05433.9276616336300.9940.05799.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F4O

5f4o


Resolution: 2.99→70.96 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.306 708 5.01 %
Rwork0.2492 13431 -
obs0.2521 14139 94.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.07 Å2 / Biso mean: 67.5565 Å2 / Biso min: 52.67 Å2
Refinement stepCycle: final / Resolution: 2.99→70.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 0 21 3318
Biso mean---65.15 -
Num. residues----425
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.99-3.220.39511440.36852729287398
3.22-3.540.39661470.310427942941100
3.54-4.060.42881120.33292104221675
4.06-5.110.24211490.193928402989100
5.11-70.960.2491560.206329643120100

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