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- PDB-22wz: GII.23/24/25 noroviruses recognize glycans via a conventional gly... -

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Basic information

Entry
Database: PDB / ID: 22wz
TitleGII.23/24/25 noroviruses recognize glycans via a conventional glycan-binding site
ComponentsVP1
KeywordsVIRAL PROTEIN / GII.25
Biological speciesNorovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLi, H.B. / Cong, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100111 China
CitationJournal: Front Microbiol / Year: 2026
Title: GII.23/24/25 noroviruses recognize glycans via a conventional glycan-binding site.
Authors: Li, H. / Cong, X. / Sun, X. / Qi, J. / Li, X. / Jin, M. / Duan, Z.
History
DepositionJan 26, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
B: VP1


Theoretical massNumber of molelcules
Total (without water)68,0862
Polymers68,0862
Non-polymers00
Water13,799766
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-11 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.839, 53.491, 109.425
Angle α, β, γ (deg.)90.00, 102.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein VP1


Mass: 34043.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.17M ammonium sulfate, 0.085 M sodium cacodylate trihydrate (pH 6.5), 25.5% (w/v) PEG 8,000, and 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.491→47.771 Å / Num. obs: 99331 / % possible obs: 97.87 % / Redundancy: 6.6 % / CC1/2: 0.853 / Net I/σ(I): 2.955
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 9821 / CC1/2: 0.853

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Processing

Software
NameVersionClassification
PHENIXPHENIXrefinement
AutoProcessPDB_EXTRACTdata reduction
HKL-2000HKL-2000data scaling
PHENIXPHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→45.31 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2025 --
Rwork0.1837 --
obs-98098 97.87 %
Refinement stepCycle: LAST / Resolution: 1.5→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4806 0 0 766 5572

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