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

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Basic information

Entry
Database: PDB / ID: 22xh
TitleGII.23/24/25 noroviruses recognize glycans via a conventional glycan-binding site
ComponentsVP1
KeywordsVIRAL PROTEIN / GII.25 P domain / H disaccharide
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: 1.6 Å
AuthorsDuan, Z.J. / Cong, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) 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 27, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 25, 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

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7394
Polymers68,0862
Non-polymers6532
Water12,304683
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint2 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.950, 53.392, 109.355
Angle α, β, γ (deg.)90.00, 102.90, 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 GII / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H4Y935
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-2DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a1221m-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(2+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 45.98 %
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: 0.97892 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 80852 / % possible obs: 98.54 % / Redundancy: 5.5 % / CC1/2: 0.811 / Net I/σ(I): 2.454
Reflection shellResolution: 1.6→1.66 Å / Num. unique obs: 7979 / CC1/2: 0.808

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Processing

Software
NameVersionClassification
PHENIXPHENIXrefinement
HKL-2000HKL-2000data reduction
HKL-2000HKL-2000data scaling
PHENIXPHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→47.7 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1966 4031 -
Rwork0.1801 --
obs-80852 99.7 %
Refinement stepCycle: LAST / Resolution: 1.6→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4806 0 44 683 5533
LS refinement shellResolution: 1.595→1.652 Å
RfactorNum. reflection
Rfree0.2428 -
Rwork0.2324 -
obs-7210

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