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- PDB-8vrv: GII.4c H2-tri HBGA norovirus protruding domain -

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Basic information

Entry
Database: PDB / ID: 8vrv
TitleGII.4c H2-tri HBGA norovirus protruding domain
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / norovirus
Function / homology
Function and homology information


virion component / host cell cytoplasm
Similarity search - Function
Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
FORMIC ACID / Capsid protein
Similarity search - Component
Biological speciesNorovirus GII.4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsKher, G. / Prewitt, A. / Pancera, M. / Hansman, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
CitationJournal: J.Virol. / Year: 2024
Title: Development of a broad-spectrum therapeutic Fc-nanobody for human noroviruses.
Authors: Hansman, G.S. / Kher, G. / Svirina, A.D. / Tame, J.R.H. / Hartley-Tassell, L. / Irie, H. / Haselhorst, T. / von Itzstein, M. / Rudd, P.A. / Pancera, M.
History
DepositionJan 22, 2024Deposition site: RCSB / Processing site: RCSB
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: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,17212
Polymers67,3352
Non-polymers83710
Water12,052669
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint6 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.666, 90.470, 91.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Capsid protein


Mass: 33667.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII.4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A168DBN0
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: SG1 1-24 0.2 M Magnesium formate dihydrate 20% 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: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.61→49.26 Å / Num. obs: 82708 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Χ2: 0.56 / Net I/σ(I): 11.7 / Num. measured all: 562066
Reflection shellResolution: 1.61→1.64 Å / % possible obs: 98.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.797 / Num. measured all: 26494 / Num. unique obs: 3989 / CC1/2: 0.769 / Rpim(I) all: 0.326 / Rrim(I) all: 0.862 / Χ2: 0.51 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→45.67 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1849 4133 5 %
Rwork0.1565 --
obs0.1579 82627 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 55 669 5450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084916
X-RAY DIFFRACTIONf_angle_d0.9756717
X-RAY DIFFRACTIONf_dihedral_angle_d8.101672
X-RAY DIFFRACTIONf_chiral_restr0.059751
X-RAY DIFFRACTIONf_plane_restr0.009887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.630.31491360.25532539X-RAY DIFFRACTION98
1.63-1.650.25021410.20352589X-RAY DIFFRACTION100
1.65-1.670.23341250.1912595X-RAY DIFFRACTION100
1.67-1.690.22361410.192556X-RAY DIFFRACTION100
1.69-1.710.20351360.18162587X-RAY DIFFRACTION100
1.71-1.730.23241340.17932593X-RAY DIFFRACTION100
1.73-1.760.21221450.17112586X-RAY DIFFRACTION100
1.76-1.790.20711300.17152625X-RAY DIFFRACTION100
1.79-1.810.21091400.17132561X-RAY DIFFRACTION100
1.81-1.840.19791360.17022578X-RAY DIFFRACTION100
1.84-1.880.2141380.17392611X-RAY DIFFRACTION100
1.88-1.910.20891410.1652602X-RAY DIFFRACTION100
1.91-1.950.20231280.16282615X-RAY DIFFRACTION100
1.95-1.990.19611390.15992582X-RAY DIFFRACTION100
1.99-2.030.20131400.15162603X-RAY DIFFRACTION100
2.03-2.080.19271390.15552618X-RAY DIFFRACTION100
2.08-2.130.17911330.15512589X-RAY DIFFRACTION100
2.13-2.190.19321390.15192598X-RAY DIFFRACTION100
2.19-2.250.1781360.15442626X-RAY DIFFRACTION100
2.25-2.320.18971370.14822605X-RAY DIFFRACTION100
2.32-2.410.17691400.1472617X-RAY DIFFRACTION100
2.41-2.50.20131370.14862613X-RAY DIFFRACTION100
2.5-2.620.17141410.15272622X-RAY DIFFRACTION100
2.62-2.750.18551400.15742641X-RAY DIFFRACTION100
2.75-2.930.1721410.15982645X-RAY DIFFRACTION100
2.93-3.150.19781360.16242634X-RAY DIFFRACTION100
3.15-3.470.19171390.15082659X-RAY DIFFRACTION100
3.47-3.970.17041380.15262676X-RAY DIFFRACTION100
3.97-50.13821430.12222696X-RAY DIFFRACTION100
5-45.670.15831440.16222833X-RAY DIFFRACTION100

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