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- PDB-8v95: GII.8 Amsterdam norovirus protruding domain -

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Basic information

Entry
Database: PDB / ID: 8v95
TitleGII.8 Amsterdam norovirus protruding domain
ComponentsCapsid protein (Fragment)
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 / Capsid protein
Function and homology information
Biological speciesHuman calicivirus strain Hu/NLV/Amsterdam/98-18/1998/NET
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 (Fragment)
B: Capsid protein (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,9453
Polymers117,8832
Non-polymers621
Water13,025723
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-13 kcal/mol
Surface area23350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.230, 78.428, 115.387
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 (Fragment)


Mass: 58941.336 Da / Num. of mol.: 2 / Fragment: GII.8 Amsterdam P domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human calicivirus strain Hu/NLV/Amsterdam/98-18/1998/NET
Production host: Escherichia coli (E. coli) / References: UniProt: Q9PY74
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 723 / 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 Sodium chloride 0.1 M Sodium/potassium phosphate (pH 6.2) 50% v/v PEG 200

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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: 1.73→46.68 Å / Num. obs: 64062 / % possible obs: 99.2 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.04 / Rrim(I) all: 0.098 / Χ2: 0.49 / Net I/σ(I): 8.8 / Num. measured all: 375331
Reflection shellResolution: 1.73→1.76 Å / % possible obs: 86.2 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.647 / Num. measured all: 16109 / Num. unique obs: 3023 / CC1/2: 0.81 / Rpim(I) all: 0.294 / Rrim(I) all: 0.713 / Χ2: 0.3 / Net I/σ(I) obs: 1.4

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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: 1.73→46.68 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2037 3199 5 %
Rwork0.1742 --
obs0.1757 63964 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4718 0 4 723 5445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064855
X-RAY DIFFRACTIONf_angle_d0.8816632
X-RAY DIFFRACTIONf_dihedral_angle_d14.2261761
X-RAY DIFFRACTIONf_chiral_restr0.055724
X-RAY DIFFRACTIONf_plane_restr0.007892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.750.40151130.29992144X-RAY DIFFRACTION82
1.75-1.780.271390.24852645X-RAY DIFFRACTION100
1.78-1.810.27621380.23252609X-RAY DIFFRACTION100
1.81-1.840.2641370.21782626X-RAY DIFFRACTION100
1.84-1.880.26971400.21972638X-RAY DIFFRACTION100
1.88-1.910.25551380.21952645X-RAY DIFFRACTION100
1.91-1.950.25891380.20932614X-RAY DIFFRACTION100
1.95-1.990.22271390.19562652X-RAY DIFFRACTION100
1.99-2.040.25321400.17822645X-RAY DIFFRACTION100
2.04-2.090.23071390.18042630X-RAY DIFFRACTION100
2.09-2.150.20931380.17662644X-RAY DIFFRACTION100
2.15-2.210.21171390.17072629X-RAY DIFFRACTION100
2.21-2.280.19191390.18052644X-RAY DIFFRACTION100
2.28-2.360.22741400.17042657X-RAY DIFFRACTION100
2.36-2.460.21911410.17072680X-RAY DIFFRACTION100
2.46-2.570.19871400.17672646X-RAY DIFFRACTION100
2.57-2.710.21681400.18032675X-RAY DIFFRACTION100
2.71-2.870.21791400.19192652X-RAY DIFFRACTION100
2.87-3.10.2341410.18472686X-RAY DIFFRACTION100
3.1-3.410.2171420.17472699X-RAY DIFFRACTION100
3.41-3.90.18121420.1622690X-RAY DIFFRACTION100
3.9-4.910.13381440.13292748X-RAY DIFFRACTION100
4.91-46.680.15891520.14782867X-RAY DIFFRACTION100

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