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- PDB-8en4: Structure of GII.4 norovirus in complex with Nanobody 53 -

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Basic information

Entry
Database: PDB / ID: 8en4
TitleStructure of GII.4 norovirus in complex with Nanobody 53
Components
  • Nanobody 53
  • VP1
KeywordsVIRAL PROTEIN / norovirus / nanobody
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virion component / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / VP1
Function and homology information
Biological speciesNorovirus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.3Nov 20, 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
B: VP1
C: Nanobody 53
D: Nanobody 53
A: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2347
Polymers95,0484
Non-polymers1863
Water2,036113
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)108.411, 137.292, 140.176
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: Protein VP1


Mass: 34132.039 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: K4LM89
#2: Antibody Nanobody 53


Mass: 13391.939 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.: 3 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
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 PILATUS 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: 2.3→54.1 Å / Num. obs: 46757 / % possible obs: 99.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 41.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.033 / Rrim(I) all: 0.075 / Net I/σ(I): 11.8 / Num. measured all: 236322 / Scaling rejects: 561
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3850.4322240444690.9310.2110.4823.198.3
8.9-54.14.70.03541978900.9980.0170.0425.399.2

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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: 4oos

4oos


Resolution: 2.3→49.04 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 3837 4.29 %
Rwork0.2146 85578 -
obs0.216 46628 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.74 Å2 / Biso mean: 50.1943 Å2 / Biso min: 28.38 Å2
Refinement stepCycle: final / Resolution: 2.3→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6536 0 12 113 6661
Biso mean--45.24 41.01 -
Num. residues----841
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.330.39061500.34913132100
2.33-2.360.39491430.33663210100
2.36-2.390.34161360.30993149100
2.39-2.430.35281630.3177316499
2.43-2.460.3311290.2943201100
2.46-2.50.35321480.28543152100
2.5-2.540.34111400.29063204100
2.54-2.590.29981400.28063112100
2.59-2.630.38851420.27123174100
2.63-2.680.30271360.2809321099
2.68-2.740.34121360.27053168100
2.74-2.80.29031440.2793320799
2.8-2.860.33831490.2782312099
2.86-2.930.32531280.279314599
2.93-3.010.30661490.261318799
3.01-3.10.28281450.25073170100
3.1-3.20.27091370.24453180100
3.2-3.320.24921490.2403313599
3.32-3.450.26711400.2279316199
3.45-3.610.22671440.2279317599
3.61-3.80.27231430.20723144100
3.8-4.030.21041410.18863194100
4.03-4.350.22621440.16363173100
4.35-4.780.17511400.1493168100
4.78-5.470.1711430.1575317499
5.48-6.890.17931430.16753168100

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