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- PDB-8v98: GII.24 Loreto 1972 norovirus protruding domain -

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Basic information

Entry
Database: PDB / ID: 8v98
TitleGII.24 Loreto 1972 norovirus protruding domain
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / norovirus
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 / Major capsid protein
Function and homology information
Biological speciesNorovirus GII
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsKher, G. / Prewitt, A. / Pancera, M. / Hansman, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
CitationJournal: J.Virol. / Year: 2024
Title: Development of a broad-spectrum therapeutic Fc-nanobody for human noroviruses.
Authors: Hansman, G.S. / Kher, G. / Svirina, A.D. / Tame, J.R.H. / Hartley-Tassell, L. / Irie, H. / Haselhorst, T. / von Itzstein, M. / Rudd, P.A. / Pancera, M.
History
DepositionDec 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,09010
Polymers119,4602
Non-polymers6308
Water13,745763
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-0 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.751, 80.821, 70.983
Angle α, β, γ (deg.)90.00, 113.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid protein VP1


Mass: 59730.035 Da / Num. of mol.: 2 / Fragment: GII.24 Loreto 1972 P domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII / Gene: ORF2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V0QSQ1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / 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

Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: M Zinc sulfate heptahydrate M MES (pH 6.5) 25% v/v PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2023 / Details: 0.95373
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.74→45.84 Å / Num. obs: 63621 / % possible obs: 98.8 % / Redundancy: 3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.043 / Rrim(I) all: 0.076 / Χ2: 0.46 / Net I/σ(I): 12.1 / Num. measured all: 189441
Reflection shellResolution: 1.74→1.77 Å / % possible obs: 96.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.194 / Num. measured all: 10036 / Num. unique obs: 3390 / CC1/2: 0.949 / Rpim(I) all: 0.136 / Rrim(I) all: 0.239 / Χ2: 0.35 / Net I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→45.84 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1893 3168 4.99 %
Rwork0.1604 --
obs0.1618 63453 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4833 0 40 763 5636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085083
X-RAY DIFFRACTIONf_angle_d0.9576946
X-RAY DIFFRACTIONf_dihedral_angle_d13.9431886
X-RAY DIFFRACTIONf_chiral_restr0.064738
X-RAY DIFFRACTIONf_plane_restr0.011931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.770.24161240.21122520X-RAY DIFFRACTION95
1.77-1.790.24321380.1852628X-RAY DIFFRACTION99
1.79-1.820.2191400.17372638X-RAY DIFFRACTION99
1.82-1.850.22191430.17832615X-RAY DIFFRACTION99
1.85-1.890.23721310.17772627X-RAY DIFFRACTION99
1.89-1.920.27141330.23892501X-RAY DIFFRACTION93
1.93-1.960.22971410.18512621X-RAY DIFFRACTION98
1.96-2.010.21221300.17052608X-RAY DIFFRACTION100
2.01-2.050.22221350.16942637X-RAY DIFFRACTION99
2.05-2.110.20161400.1612671X-RAY DIFFRACTION100
2.11-2.160.18911360.15192631X-RAY DIFFRACTION100
2.16-2.230.1861430.15752627X-RAY DIFFRACTION100
2.23-2.30.24331340.19072446X-RAY DIFFRACTION92
2.3-2.380.18351390.15152646X-RAY DIFFRACTION100
2.38-2.470.17521420.15672674X-RAY DIFFRACTION100
2.47-2.590.19471370.15952662X-RAY DIFFRACTION100
2.59-2.720.18151400.16772651X-RAY DIFFRACTION100
2.72-2.890.18431370.16042670X-RAY DIFFRACTION100
2.89-3.120.16081390.15782615X-RAY DIFFRACTION99
3.12-3.430.17621440.14772651X-RAY DIFFRACTION99
3.43-3.930.1751400.14612606X-RAY DIFFRACTION97
3.93-4.950.14311390.13022658X-RAY DIFFRACTION99
4.95-45.840.16891430.15132682X-RAY DIFFRACTION98

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