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- PDB-8v99: GII.26 Leon 4509 norovirus protruding domain -

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Basic information

Entry
Database: PDB / ID: 8v99
TitleGII.26 Leon 4509 norovirus protruding domain
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / norovirus
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / ACETATE ION / DI(HYDROXYETHYL)ETHER / Major capsid protein
Function and homology information
Biological speciesNorovirus GII
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsKher, G. / Reese, T. / 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
DepositionDec 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: 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 1.2Jul 31, 2024Group: 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: Capsid protein VP1
B: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,94747
Polymers119,0722
Non-polymers2,87545
Water9,260514
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.436, 71.165, 78.586
Angle α, β, γ (deg.)90.00, 109.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Capsid protein VP1


Mass: 59535.848 Da / Num. of mol.: 2 / Fragment: GII.26 Leon 4509 P domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII / Production host: Escherichia coli (E. coli) / References: UniProt: A0A142KD02
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Ammonium acetate 0.1 M BIS-Tris (pH 5.5) 17% w/v PEG 10,000

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.47→43.69 Å / Num. obs: 111573 / % possible obs: 98.8 % / Redundancy: 2.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.062 / Rrim(I) all: 0.11 / Χ2: 0.47 / Net I/σ(I): 6.1 / Num. measured all: 322323
Reflection shellResolution: 1.47→1.5 Å / % possible obs: 93.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.817 / Num. measured all: 14540 / Num. unique obs: 5215 / CC1/2: 0.476 / Rpim(I) all: 0.569 / Rrim(I) all: 1 / Χ2: 0.36 / Net I/σ(I) obs: 0.9

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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: 1.47→40.66 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1871 5579 5 %
Rwork0.1483 --
obs0.1502 111559 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→40.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 186 514 5496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145076
X-RAY DIFFRACTIONf_angle_d1.2876850
X-RAY DIFFRACTIONf_dihedral_angle_d13.5471833
X-RAY DIFFRACTIONf_chiral_restr0.089745
X-RAY DIFFRACTIONf_plane_restr0.009897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.490.33791710.30743242X-RAY DIFFRACTION91
1.49-1.510.31841870.26573558X-RAY DIFFRACTION99
1.51-1.530.27781850.25553516X-RAY DIFFRACTION99
1.53-1.550.27631870.24313550X-RAY DIFFRACTION99
1.55-1.570.25721860.22243533X-RAY DIFFRACTION99
1.57-1.590.24831860.2083539X-RAY DIFFRACTION99
1.59-1.610.30431860.21663539X-RAY DIFFRACTION99
1.61-1.630.22831870.19973542X-RAY DIFFRACTION99
1.63-1.660.23011850.18753519X-RAY DIFFRACTION99
1.66-1.690.25591860.17883546X-RAY DIFFRACTION99
1.69-1.720.23691860.17093527X-RAY DIFFRACTION99
1.72-1.750.25641870.16963544X-RAY DIFFRACTION99
1.75-1.780.21391840.15653508X-RAY DIFFRACTION98
1.78-1.820.17351840.13363497X-RAY DIFFRACTION99
1.82-1.860.17791890.12583574X-RAY DIFFRACTION100
1.86-1.90.18481860.12663551X-RAY DIFFRACTION100
1.9-1.950.18881890.12433576X-RAY DIFFRACTION100
1.95-20.18111870.1233569X-RAY DIFFRACTION100
2-2.060.14471870.1243549X-RAY DIFFRACTION99
2.06-2.120.17641880.12373571X-RAY DIFFRACTION99
2.12-2.20.1831880.12143564X-RAY DIFFRACTION99
2.2-2.290.16451850.12543527X-RAY DIFFRACTION99
2.29-2.390.17491890.12063563X-RAY DIFFRACTION99
2.39-2.520.16351840.12823513X-RAY DIFFRACTION98
2.52-2.680.17931860.13453534X-RAY DIFFRACTION98
2.68-2.880.16781880.13743562X-RAY DIFFRACTION99
2.88-3.170.16321870.13713559X-RAY DIFFRACTION99
3.17-3.630.16131870.13813560X-RAY DIFFRACTION98
3.63-4.580.13961860.13483530X-RAY DIFFRACTION98
4.58-40.660.2011860.16893518X-RAY DIFFRACTION95

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