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- PDB-8v97: GII.17 CS-E1 norovirus protruding domain -

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Basic information

Entry
Database: PDB / ID: 8v97
TitleGII.17 CS-E1 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 / DI(HYDROXYETHYL)ETHER / Capsid protein
Function and homology information
Biological speciesNorovirus GII
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 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
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

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,51510
Polymers117,9742
Non-polymers5418
Water15,493860
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint14 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.333, 72.025, 81.870
Angle α, β, γ (deg.)90.00, 111.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid protein VP1


Mass: 58987.137 Da / Num. of mol.: 2 / Fragment: GII.17 CS-E1 P domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII / Production host: Escherichia coli (E. coli) / References: UniProt: Q6EAX3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / 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: 0.2 M TMAO 0.1 M Tris (pH 8.5) 50% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.27→45.26 Å / Num. obs: 177052 / % possible obs: 99.7 % / Redundancy: 5.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.025 / Rrim(I) all: 0.059 / Χ2: 0.48 / Net I/σ(I): 12.8 / Num. measured all: 934353
Reflection shellResolution: 1.27→1.29 Å / % possible obs: 94.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.312 / Num. measured all: 41548 / Num. unique obs: 8244 / CC1/2: 0.927 / Rpim(I) all: 0.152 / Rrim(I) all: 0.349 / Χ2: 0.35 / Net I/σ(I) obs: 3

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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: 1.27→45.26 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.172 8858 5 %
Rwork0.1618 --
obs0.1623 177018 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.27→45.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4740 0 35 860 5635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054960
X-RAY DIFFRACTIONf_angle_d0.8346782
X-RAY DIFFRACTIONf_dihedral_angle_d13.1251796
X-RAY DIFFRACTIONf_chiral_restr0.083750
X-RAY DIFFRACTIONf_plane_restr0.009904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.280.20972780.20435159X-RAY DIFFRACTION92
1.28-1.30.19253060.18555646X-RAY DIFFRACTION100
1.3-1.320.19052790.17665545X-RAY DIFFRACTION100
1.32-1.330.19152910.18035612X-RAY DIFFRACTION100
1.33-1.350.20053090.17745558X-RAY DIFFRACTION100
1.35-1.370.19642790.18475625X-RAY DIFFRACTION100
1.37-1.390.19333040.17815648X-RAY DIFFRACTION100
1.39-1.410.18042960.17135582X-RAY DIFFRACTION100
1.41-1.430.18743010.17235596X-RAY DIFFRACTION100
1.43-1.450.16152940.16065639X-RAY DIFFRACTION100
1.45-1.480.16782740.16355573X-RAY DIFFRACTION100
1.48-1.510.16883100.15755607X-RAY DIFFRACTION100
1.51-1.530.16962910.15795621X-RAY DIFFRACTION100
1.54-1.570.18113000.15965623X-RAY DIFFRACTION100
1.57-1.60.16343010.15985612X-RAY DIFFRACTION100
1.6-1.640.16852810.15655632X-RAY DIFFRACTION100
1.64-1.680.19722990.16675586X-RAY DIFFRACTION100
1.68-1.720.1763000.16835611X-RAY DIFFRACTION100
1.72-1.770.17153000.16215619X-RAY DIFFRACTION100
1.77-1.830.17223020.16125610X-RAY DIFFRACTION100
1.83-1.90.17622920.16245630X-RAY DIFFRACTION100
1.9-1.970.1822960.16455599X-RAY DIFFRACTION100
1.97-2.060.17233000.16325635X-RAY DIFFRACTION100
2.06-2.170.17052970.16115604X-RAY DIFFRACTION100
2.17-2.310.16613020.15955647X-RAY DIFFRACTION100
2.31-2.490.18222930.16455662X-RAY DIFFRACTION100
2.49-2.740.1842890.17445626X-RAY DIFFRACTION100
2.74-3.130.16892940.17225670X-RAY DIFFRACTION100
3.13-3.950.16042970.14695645X-RAY DIFFRACTION100
3.95-45.260.14973030.14285738X-RAY DIFFRACTION99

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