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- PDB-8en6: Structure of GII.4 norovirus in complex with Nanobody 76 -

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Basic information

Entry
Database: PDB / ID: 8en6
TitleStructure of GII.4 norovirus in complex with Nanobody 76
Components
  • GII.4 P domain
  • Nanobody 76
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 / ISOPROPYL ALCOHOL / VP1
Function and homology information
Biological speciesNorovirus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.1Mar 22, 2023Group: Structure summary / Category: entity / struct / Item: _entity.pdbx_description / _struct.title
Revision 1.2Sep 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 1.3Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Oct 23, 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: GII.4 P domain
C: Nanobody 76
B: GII.4 P domain
D: Nanobody 76
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,66919
Polymers94,5754
Non-polymers1,09315
Water15,709872
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)74.412, 119.706, 127.816
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Antibody , 2 types, 4 molecules ABCD

#1: Protein GII.4 P domain


Mass: 34074.988 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 76


Mass: 13212.732 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)

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Non-polymers , 5 types, 887 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 872 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 17% [w/v] PEG4000, 0.0095 M HEPES [pH 7.5], 8.5% [v/v] isopropanol, and 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→87.37 Å / Num. obs: 171712 / % possible obs: 99.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 11.67 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.044 / Rrim(I) all: 0.094 / Net I/σ(I): 9.3 / Num. measured all: 754982 / Scaling rejects: 1404
Reflection shell

Diffraction-ID: 1 / % possible all: 98.4

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.53-1.5640.7513321183300.6390.4190.8641.5
8.38-87.374.40.028519111680.9970.0150.03327.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4oos

4oos


Resolution: 1.6→64.31 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 7305 4.86 %
Rwork0.173 142950 -
obs0.174 150255 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.54 Å2 / Biso mean: 17.6947 Å2 / Biso min: 4.09 Å2
Refinement stepCycle: final / Resolution: 1.6→64.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6656 0 100 872 7628
Biso mean--27.14 25.19 -
Num. residues----855
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.620.24652270.231548055032100
1.62-1.640.26832400.222546884928100
1.64-1.660.25182320.217347374969100
1.66-1.680.22932130.204247464959100
1.68-1.70.2292390.202547534992100
1.7-1.720.22842340.196846864920100
1.72-1.750.21822260.194347334959100
1.75-1.770.21022250.19074756498199
1.77-1.80.20532410.19174682492399
1.8-1.830.23192380.18924688492699
1.83-1.860.20332400.190847544994100
1.86-1.90.23212720.187746954967100
1.9-1.930.21472250.181547554980100
1.93-1.970.20642540.168547354989100
1.97-2.020.17142600.162347354995100
2.02-2.060.19322430.162147284971100
2.06-2.110.18232560.162247394995100
2.11-2.170.17792700.167747445014100
2.17-2.240.18872530.164847485001100
2.24-2.310.20582740.170947244998100
2.31-2.390.21322390.175447805019100
2.39-2.490.20342580.17547575015100
2.49-2.60.20272520.178347625014100
2.6-2.740.20692750.175247665041100
2.74-2.910.19372270.176848005027100
2.91-3.130.17972340.171648525086100
3.13-3.450.18762490.16824787503699
3.45-3.950.16252210.159748805101100
3.95-4.970.15712730.139548905163100
4.97-64.310.17792150.16865045526098

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