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- PDB-7yqb: Functional and Structural Characterization of Norovirus GII.6 in ... -

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Basic information

Entry
Database: PDB / ID: 7yqb
TitleFunctional and Structural Characterization of Norovirus GII.6 in Recognizing Histo-blood Group Antigens
ComponentsVP1
KeywordsVIRAL PROTEIN / proein
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: 1.704 Å
AuthorsCong, X. / Duan, Z.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Virol Sin / Year: 2023
Title: Functional and structural characterization of Norovirus GII.6 in recognizing histo-blood group antigens.
Authors: Cong, X. / Li, H.B. / Sun, X.M. / Qi, J.X. / Zhang, Q. / Duan, Z.J. / Xu, Y. / Liu, W.L.
History
DepositionAug 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)69,6722
Polymers69,6722
Non-polymers00
Water12,791710
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-15 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.444, 94.777, 109.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein VP1 / norovirus P domain protein


Mass: 34835.855 Da / Num. of mol.: 2 / Mutation: Q304P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII / Gene: ORF2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2U9GLY1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / 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: 2.31 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium chloride dihydrate, 0.1 M sodium acetate trihydrate pH4.6, 20% (vol/vol) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 71255 / % possible obs: 92.72 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 24.843
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 66173 / CC1/2: 0.1

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RLZ

4rlz


Resolution: 1.704→47.389 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1943 3308 5 %
Rwork0.1725 62865 -
obs0.1735 66173 92.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.7 Å2 / Biso mean: 18.8428 Å2 / Biso min: 4.03 Å2
Refinement stepCycle: final / Resolution: 1.704→47.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4656 0 0 710 5366
Biso mean---26.79 -
Num. residues----599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.728-1.75380.22971090.221185367
1.7538-1.78120.2418980.2022200971
1.7812-1.81040.2151050.1965212877
1.8104-1.84160.20191120.1908227380
1.8751-1.91110.20321230.1958251490
1.9111-1.95020.26081450.1897264594
1.9502-1.99260.19471340.1881271997
1.9926-2.03890.1921410.184273398
2.0389-2.08990.19511480.17462807100
2.0899-2.14640.21251740.17762798100
2.1464-2.20960.21971300.17632822100
2.2096-2.28090.23141670.17192790100
2.2809-2.36240.19861500.17012803100
2.3624-2.4570.1781410.17612825100
2.457-2.56880.19941500.18092824100
2.5688-2.70420.21161440.18222845100
2.7042-2.87360.21341400.18562839100
2.8736-3.09550.19361220.172860100
3.0955-3.40690.17041570.16382864100
3.4069-3.89970.19221440.15132889100
3.8997-4.91240.14281590.13562890100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.177-0.09520.00210.32790.17410.6841-0.0142-0.01540.00720.04210.0266-0.029-0.03440.0116-0.060.05240.0025-0.00480.0562-0.00240.067280.7992102.251324.5242
20.2601-0.0710.12950.2373-0.07270.49360.01080.01360.0026-0.04520.00960.02180.0485-0.0528-0.01270.0591-0.00350.00120.0658-0.00210.06570.09494.56044.6354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA4 - 317
2X-RAY DIFFRACTION2chain BB4 - 317

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