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- PDB-9edp: GVIII-Chiba040502 norovirus protruding domain -

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Basic information

Entry
Database: PDB / ID: 9edp
TitleGVIII-Chiba040502 norovirus protruding domain
ComponentsVP1
KeywordsVIRAL PROTEIN / norovirus / P domain
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 / Capsid protein
Function and homology information
Biological speciesChiba-040502 virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsHolroyd, D.L. / Kumar, A. / Bruning, J.B. / Hansman, G.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Virol. / Year: 2025
Title: Antigenic structural analysis of bat and human norovirus protruding (P) domains.
Authors: Holroyd, D.L. / Kumar, A. / Vasquez, E. / Masic, V. / von Itzstein, M. / Bruning, J.B. / Hansman, G.S.
History
DepositionNov 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 23, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6652
Polymers35,6301
Non-polymers351
Water11,980665
1
A: VP1
hetero molecules

A: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3304
Polymers71,2602
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3520 Å2
ΔGint-37 kcal/mol
Surface area24520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.241, 107.241, 61.577
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-702-

HOH

21A-812-

HOH

31A-957-

HOH

41A-1059-

HOH

51A-1298-

HOH

61A-1306-

HOH

71A-1310-

HOH

81A-1344-

HOH

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Components

#1: Protein VP1


Mass: 35629.793 Da / Num. of mol.: 1 / Fragment: protruding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chiba-040502 virus / Strain: GVIII / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q3V574
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris (pH 5.5), 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.76→46.44 Å / Num. obs: 40834 / % possible obs: 99.9 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.029 / Rrim(I) all: 0.108 / Χ2: 0.57 / Net I/σ(I): 15.4 / Num. measured all: 563727
Reflection shellResolution: 1.76→1.79 Å / % possible obs: 99 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.992 / Num. measured all: 31242 / Num. unique obs: 2291 / CC1/2: 0.843 / Rpim(I) all: 0.273 / Rrim(I) all: 1.03 / Χ2: 0.53 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.8data scaling
XDSdata reduction
PHASER9.0.002phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→46.44 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1807 1998 4.9 %
Rwork0.1395 --
obs0.1415 40809 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 1 665 3060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062682
X-RAY DIFFRACTIONf_angle_d0.8213697
X-RAY DIFFRACTIONf_dihedral_angle_d11.8321037
X-RAY DIFFRACTIONf_chiral_restr0.058399
X-RAY DIFFRACTIONf_plane_restr0.007500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.25911390.22012694X-RAY DIFFRACTION99
1.8-1.850.25491420.18732758X-RAY DIFFRACTION100
1.85-1.90.21661430.17252752X-RAY DIFFRACTION100
1.91-1.970.19371440.15792727X-RAY DIFFRACTION100
1.97-2.040.20951420.16362769X-RAY DIFFRACTION100
2.04-2.120.17911410.14642749X-RAY DIFFRACTION100
2.12-2.210.18921440.14592749X-RAY DIFFRACTION100
2.21-2.330.19891440.14162788X-RAY DIFFRACTION100
2.33-2.480.19541400.14872775X-RAY DIFFRACTION100
2.48-2.670.17781400.14282757X-RAY DIFFRACTION100
2.67-2.940.17551470.1492782X-RAY DIFFRACTION100
2.94-3.360.17881400.12412790X-RAY DIFFRACTION100
3.36-4.240.14621470.11272817X-RAY DIFFRACTION100
4.24-46.440.16421450.12582904X-RAY DIFFRACTION100

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