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- PDB-5j3o: Protruding domain of GII.4 human norovirus NSW0514 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5j3o
TitleProtruding domain of GII.4 human norovirus NSW0514 in complex with 3-fucosyllactose (3FL)
ComponentsVP1
KeywordsVIRAL PROTEIN / Viral capsid protein / Protruding domain / Norovirus / Human milk oligosaccharides
Function / homology
Function and homology information


virion component / host cell cytoplasm
Similarity search - Function
Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / VP1
Similarity search - Component
Biological speciesNorovirus Hu/GII.4/Sydney/NSW0514/2012/AU
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsSingh, B.K. / Hansman, G.S.
CitationJournal: To be published
Title: Structural basis for GII.4 norovirus inhibition by human milk oligosaccharides.
Authors: Singh, B.K. / Hansman, G.S.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)69,13110
Polymers68,4302
Non-polymers7018
Water13,457747
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint12 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.070, 55.570, 115.510
Angle α, β, γ (deg.)90.000, 107.280, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein VP1


Mass: 34215.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Plasmid: MBP-HTSHP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K4LM89
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 747 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.32→42.72 Å / Num. obs: 137290 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Net I/σ(I): 8.17
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.32-1.350.3652.26169.9
1.35-1.390.3382.82193.5
1.39-1.430.33.49198.8
1.43-1.470.2694.36199.8
1.47-1.520.2185.2199.8
1.52-1.570.1925.94199.8
1.57-1.630.1676.53199.6
1.63-1.70.1577.3199.7
1.7-1.780.1398.17199.7
1.78-1.860.1179.4199.8
1.86-1.960.09810.32199.8
1.96-2.080.09711.45199.6
2.08-2.230.0911.79199.5
2.23-2.410.07812.33199.7
2.41-2.630.0712.95199.6
2.63-2.950.07414.12199.7
2.95-3.40.06314.97199.6
3.4-4.170.07814.89199.4
4.17-5.890.06515.95199.8
5.890.0616.16199.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OOS

4oos


Resolution: 1.47→42.716 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 46.41
RfactorNum. reflection% reflection
Rfree0.2005 5062 5 %
Rwork0.1716 --
obs0.173 101291 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 41.64 Å2 / Biso mean: 11.2991 Å2 / Biso min: 2.02 Å2
Refinement stepCycle: final / Resolution: 1.47→42.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 46 747 5605
Biso mean--22.58 21.75 -
Num. residues----618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075210
X-RAY DIFFRACTIONf_angle_d1.2627166
X-RAY DIFFRACTIONf_chiral_restr0.079788
X-RAY DIFFRACTIONf_plane_restr0.007962
X-RAY DIFFRACTIONf_dihedral_angle_d12.6561946
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.48670.28141670.26373175334299
1.4867-1.50420.28881700.257232193389100
1.5042-1.52250.28941660.2483163332999
1.5225-1.54180.27421710.23713231340299
1.5418-1.56210.26291650.23083123328899
1.5621-1.58350.26361690.22453267343699
1.5835-1.60610.23981660.21663138330499
1.6061-1.63010.25431700.2233212338299
1.6301-1.65560.29311680.21353177334599
1.6556-1.68270.25321700.204632203390100
1.6827-1.71170.22991670.20183200336799
1.7117-1.74290.22461680.1943203337199
1.7429-1.77640.21690.19633228339799
1.7764-1.81260.21961670.180931533320100
1.8126-1.85210.19411700.17743218338899
1.8521-1.89510.19831710.17993228339999
1.8951-1.94250.20161660.177532153381100
1.9425-1.99510.20461660.1713186335299
1.9951-2.05380.19711680.1653188335699
2.0538-2.12010.20821690.158532213390100
2.1201-2.19580.19791680.16373201336999
2.1958-2.28370.16761700.15343204337499
2.2837-2.38770.18391700.14813216338699
2.3877-2.51350.161700.151532323402100
2.5135-2.6710.19521690.15143230339999
2.671-2.87720.17541690.149632073376100
2.8772-3.16660.1711700.14673251342199
3.1666-3.62460.18481710.14653245341699
3.6246-4.56580.14531730.13283270344399
4.5658-42.73370.16071690.14793208337795

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