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- PDB-9edn: GII.23: Loreto1847 norovirus protruding domain -

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Basic information

Entry
Database: PDB / ID: 9edn
TitleGII.23: Loreto1847 norovirus protruding domain
ComponentsVP1
KeywordsVIRAL PROTEIN / norovirus / P domain
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 GII
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsHolroyd, D.L. / Kumar, A. / Bruning, J.B. / Hansman, G.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Virol. / Year: 2025
Title: Antigenic structural analysis of bat and human norovirus protruding (P) domains.
Authors: Holroyd, D.L. / Kumar, A. / Vasquez, E. / Masic, V. / von Itzstein, M. / Bruning, J.B. / Hansman, G.S.
History
DepositionNov 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: 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
Revision 1.2Apr 23, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,01122
Polymers68,8492
Non-polymers1,16220
Water24,2301345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-7 kcal/mol
Surface area25200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.140, 80.960, 71.790
Angle α, β, γ (deg.)90.00, 113.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VP1


Mass: 34424.496 Da / Num. of mol.: 2 / Fragment: protruding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII / Strain: GII.23/Loreto1847 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0U2T5K7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1345 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate (pH 4.6), 8% w/v PEG 4000

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.21→45.59 Å / Num. obs: 185707 / % possible obs: 97.3 % / Redundancy: 3.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.071 / Rrim(I) all: 0.141 / Χ2: 0.43 / Net I/σ(I): 7.8
Reflection shellResolution: 1.21→1.23 Å / % possible obs: 60.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.695 / Num. measured all: 19626 / Num. unique obs: 5677 / CC1/2: 0.688 / Rpim(I) all: 0.396 / Rrim(I) all: 0.803 / Χ2: 0.31 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.8data scaling
XDSdata reduction
PHASER9.0.002phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→40.48 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1463 9286 5 %
Rwork0.1226 --
obs0.1238 185707 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.22→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4850 0 71 1345 6266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075391
X-RAY DIFFRACTIONf_angle_d17419
X-RAY DIFFRACTIONf_dihedral_angle_d11.9772065
X-RAY DIFFRACTIONf_chiral_restr0.086801
X-RAY DIFFRACTIONf_plane_restr0.011997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.230.19972860.15855437X-RAY DIFFRACTION93
1.23-1.250.18223070.14665853X-RAY DIFFRACTION99
1.25-1.260.18853080.14835853X-RAY DIFFRACTION99
1.26-1.280.16793130.14525938X-RAY DIFFRACTION100
1.28-1.30.18893070.14445837X-RAY DIFFRACTION100
1.3-1.310.17223100.14425888X-RAY DIFFRACTION100
1.31-1.330.18193100.14585883X-RAY DIFFRACTION100
1.33-1.350.18223110.14795899X-RAY DIFFRACTION100
1.35-1.370.16683080.15035856X-RAY DIFFRACTION100
1.37-1.40.1723120.13745921X-RAY DIFFRACTION100
1.4-1.420.173090.13035868X-RAY DIFFRACTION100
1.42-1.450.16823080.12995861X-RAY DIFFRACTION100
1.45-1.470.15063110.1215901X-RAY DIFFRACTION100
1.47-1.510.14553120.11545926X-RAY DIFFRACTION100
1.51-1.540.153070.11445841X-RAY DIFFRACTION100
1.54-1.570.15263100.11655884X-RAY DIFFRACTION100
1.57-1.610.13773120.11375916X-RAY DIFFRACTION100
1.61-1.660.14613120.12025923X-RAY DIFFRACTION100
1.66-1.710.15763100.12245888X-RAY DIFFRACTION100
1.71-1.760.14233090.1235884X-RAY DIFFRACTION100
1.76-1.820.14653090.12585881X-RAY DIFFRACTION100
1.82-1.90.14183100.12335888X-RAY DIFFRACTION100
1.9-1.980.13353110.12125906X-RAY DIFFRACTION100
1.98-2.090.12283120.11445910X-RAY DIFFRACTION100
2.09-2.220.12863100.1125893X-RAY DIFFRACTION100
2.22-2.390.12933120.1115930X-RAY DIFFRACTION100
2.39-2.630.14563120.11945922X-RAY DIFFRACTION100
2.63-3.010.13073120.11935925X-RAY DIFFRACTION99
3.01-3.790.13043100.10815907X-RAY DIFFRACTION99
3.79-40.480.1533160.1266002X-RAY DIFFRACTION99

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