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- PDB-8en3: Structure of GII.17 norovirus in complex with Nanobody 45 -

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Basic information

Entry
Database: PDB / ID: 8en3
TitleStructure of GII.17 norovirus in complex with Nanobody 45
Components
  • Capsid protein VP1
  • Nanobody 45
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 / VP1
Function and homology information
Biological speciesNorovirus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP1
C: Nanobody 45
D: Nanobody 45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3896
Polymers100,2654
Non-polymers1242
Water7,548419
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)79.495, 71.306, 82.615
Angle α, β, γ (deg.)90.000, 113.320, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Gene: VP1, ORF2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S1Z370
#2: Antibody Nanobody 45


Mass: 15817.297 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.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: (1.6 M ammonium sulfate, 0.08 M sodium acetate, and 20% [v/v] glycerol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 49644 / % possible obs: 99.8 % / Redundancy: 6.103 % / Biso Wilson estimate: 20.02 Å2 / CC1/2: 0.974 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.236.3781.0461.5479780.6271.13999.7
2.23-2.386.8640.842.0674780.7480.9199.8
2.38-2.577.230.7352.4669690.7980.79299.8
2.57-2.827.1140.5443.3464520.8830.58799.8
2.82-3.156.7470.3545.0358290.9440.38499.8
3.15-3.636.740.218.1251770.980.22899.7
3.63-4.447.2210.13712.5843990.9930.14899.9
4.44-6.266.6460.1411.7334050.9910.15299.7

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Processing

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

5f4o


Resolution: 2.1→44.53 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 2000 4.03 %
Rwork0.2126 47614 -
obs0.2146 49614 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.76 Å2 / Biso mean: 21.0581 Å2 / Biso min: 5.67 Å2
Refinement stepCycle: final / Resolution: 2.1→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6739 0 8 419 7166
Biso mean--29.38 21.65 -
Num. residues----861
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 (%)
2.1-2.150.29751540.25023355350999
2.15-2.210.32221370.24433513488100
2.21-2.280.28861440.237734163560100
2.28-2.350.33811400.238133533493100
2.35-2.430.26791430.239734193562100
2.43-2.530.33541330.23933803513100
2.53-2.650.32841460.235933893535100
2.65-2.790.28071400.234933973537100
2.79-2.960.2681390.231634093548100
2.96-3.190.29841440.216934013545100
3.19-3.510.23811420.209533943536100
3.51-4.020.19211470.17734233570100
4.02-5.060.22011440.161734253569100
5.06-44.530.23271470.206735023649100

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