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- PDB-8y6d: Norovirus GII.10 P domain and 2'-FL (tablet) -

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Basic information

Entry
Database: PDB / ID: 8y6d
TitleNorovirus GII.10 P domain and 2'-FL (tablet)
ComponentsGII.10 norovirus P domain in complex with 2'-FL (tablet)
KeywordsVIRAL PROTEIN / Sugar / complex / milk oligosaccharide
Function / homologyNITRATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesNorovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsHansman, G. / Tame, J.R.H. / Kher, G. / Pancera, M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Virol. / Year: 2024
Title: Human milk oligosaccharide 2'-fucosyllactose guards norovirus histo-blood group antigen co-factor binding site.
Authors: Rudd, P.A. / Kher, G. / Tame, J.R.H. / Irie, H. / Haselhorst, T. / von Itzstein, M. / Pancera, M. / Hansman, G.S.
History
DepositionFeb 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _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.10 norovirus P domain in complex with 2'-FL (tablet)
B: GII.10 norovirus P domain in complex with 2'-FL (tablet)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,29115
Polymers69,0132
Non-polymers1,27713
Water10,755597
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint2 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.408, 78.926, 70.074
Angle α, β, γ (deg.)90.00, 101.13, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein GII.10 norovirus P domain in complex with 2'-FL (tablet)


Mass: 34506.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE GENEBANK ACCESSION NUMBER IS AF504671 FOR THIS PROTEIN.
Source: (gene. exp.) Norovirus / Production host: Escherichia coli (E. coli)
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 609 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: NO3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium nitrate 0.1 M bis-tris propane (pH 7.5) 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.41→43.55 Å / Num. obs: 133866 / % possible obs: 99.4 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.031 / Rrim(I) all: 0.067 / Χ2: 0.49 / Net I/σ(I): 9 / Num. measured all: 608864
Reflection shellResolution: 1.41→1.43 Å / % possible obs: 93.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 1.261 / Num. measured all: 26159 / Num. unique obs: 6219 / CC1/2: 0.506 / Rpim(I) all: 0.673 / Rrim(I) all: 1.435 / Χ2: 0.37 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→43.55 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1949 6670 4.99 %
Rwork0.1708 --
obs0.172 133778 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.41→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4755 0 84 597 5436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094976
X-RAY DIFFRACTIONf_angle_d1.0086805
X-RAY DIFFRACTIONf_dihedral_angle_d12.8271776
X-RAY DIFFRACTIONf_chiral_restr0.181774
X-RAY DIFFRACTIONf_plane_restr0.011890
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.430.37711890.38173899X-RAY DIFFRACTION91
1.43-1.440.37862120.34894205X-RAY DIFFRACTION100
1.44-1.460.3242540.31764240X-RAY DIFFRACTION100
1.46-1.480.28731990.2914208X-RAY DIFFRACTION100
1.48-1.50.3142300.2794251X-RAY DIFFRACTION100
1.5-1.520.23862210.25694269X-RAY DIFFRACTION100
1.52-1.540.26612230.24374225X-RAY DIFFRACTION100
1.54-1.560.26922400.23824250X-RAY DIFFRACTION100
1.56-1.590.25112090.22834219X-RAY DIFFRACTION100
1.59-1.610.25182170.2214253X-RAY DIFFRACTION100
1.61-1.640.24912290.21834262X-RAY DIFFRACTION100
1.64-1.670.23252330.21594241X-RAY DIFFRACTION100
1.67-1.70.21582060.1994262X-RAY DIFFRACTION100
1.7-1.740.22842350.1924219X-RAY DIFFRACTION100
1.74-1.780.22392210.1844274X-RAY DIFFRACTION100
1.78-1.820.2162300.17844234X-RAY DIFFRACTION100
1.82-1.860.19652130.17684270X-RAY DIFFRACTION100
1.86-1.910.212240.17634254X-RAY DIFFRACTION100
1.91-1.970.18612230.17424242X-RAY DIFFRACTION100
1.97-2.030.19692340.17594237X-RAY DIFFRACTION100
2.03-2.110.20022130.17184277X-RAY DIFFRACTION100
2.11-2.190.18572230.16184269X-RAY DIFFRACTION100
2.19-2.290.17872230.16284223X-RAY DIFFRACTION100
2.29-2.410.19112220.15444247X-RAY DIFFRACTION100
2.41-2.560.17892270.15824254X-RAY DIFFRACTION99
2.56-2.760.19482180.16734248X-RAY DIFFRACTION99
2.76-3.040.18262270.1614229X-RAY DIFFRACTION99
3.04-3.480.19772190.15324249X-RAY DIFFRACTION99
3.48-4.380.15272320.13354270X-RAY DIFFRACTION99
4.38-43.550.16582240.14884328X-RAY DIFFRACTION99

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