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- PDB-6gw0: GII.1 human norovirus protruding domain in complex with taurochen... -

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Basic information

Entry
Database: PDB / ID: 6gw0
TitleGII.1 human norovirus protruding domain in complex with taurochenodeoxycholate (TCDCA)
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / Norovirus / GII.1 / P domain / TCDCA / HBGA
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
TAUROCHENODEOXYCHOLIC ACID / Capsid protein VP1
Similarity search - Component
Biological speciesNorovirus Hu/GII.1/7EK/Hawaii/1971/USA
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKilic, T. / Hansman, G.S.
CitationJournal: J. Virol. / Year: 2019
Title: Structural Basis for Human Norovirus Capsid Binding to Bile Acids.
Authors: Kilic, T. / Koromyslova, A. / Hansman, G.S.
History
DepositionJun 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2352
Polymers34,7361
Non-polymers5001
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-1 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.450, 99.200, 79.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-782-

HOH

21A-801-

HOH

31A-804-

HOH

41A-860-

HOH

51A-939-

HOH

61A-954-

HOH

71A-989-

HOH

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Components

#1: Protein Capsid protein VP1


Mass: 34735.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal GPGS is part of an expression tag. / Source: (gene. exp.) Norovirus Hu/GII.1/7EK/Hawaii/1971/USA / Gene: VP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J9XXB7
#2: Chemical ChemComp-TUD / TAUROCHENODEOXYCHOLIC ACID / 2-(((3ALPHA,5BETA,7ALPHA)-3,7-DIHYDROXY-24-OXOCHOLAN-24-YL)AMINO)ETHANESULFONIC ACID / TAUROCHENODEOXYCHOLATE


Mass: 499.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H45NO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0,1 M Magnesium acetate tetrahydrate 0,1 M Sodium citrate 5,8 14 % w/v PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.4→59.55 Å / Num. obs: 57934 / % possible obs: 99.74 % / Redundancy: 13.2 % / Biso Wilson estimate: 13.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03736 / Rpim(I) all: 0.0106 / Rrim(I) all: 0.03887 / Net I/σ(I): 41.85
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.4668 / Mean I/σ(I) obs: 4.93 / Num. unique obs: 5641 / CC1/2: 0.95 / Rpim(I) all: 0.1578 / Rrim(I) all: 0.4937 / % possible all: 98.34

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSVERSION Jun 1, 2017data reduction
XSCALEVERSION Jun 1, 2017data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ROX

4rox


Resolution: 1.4→33.692 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.45
RfactorNum. reflection% reflection
Rfree0.1676 2898 5 %
Rwork0.1485 --
obs0.1495 57927 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→33.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 34 310 2690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072488
X-RAY DIFFRACTIONf_angle_d0.8833438
X-RAY DIFFRACTIONf_dihedral_angle_d13.719893
X-RAY DIFFRACTIONf_chiral_restr0.081387
X-RAY DIFFRACTIONf_plane_restr0.007453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3985-1.42140.35081310.36152471X-RAY DIFFRACTION95
1.4214-1.44590.22591360.22722595X-RAY DIFFRACTION100
1.4459-1.47220.18061380.16532621X-RAY DIFFRACTION100
1.4722-1.50050.19581360.15632573X-RAY DIFFRACTION100
1.5005-1.53120.16961380.15622623X-RAY DIFFRACTION100
1.5312-1.56450.18191360.15962590X-RAY DIFFRACTION100
1.5645-1.60090.16561380.13732612X-RAY DIFFRACTION100
1.6009-1.64090.17331360.13992592X-RAY DIFFRACTION100
1.6409-1.68530.18311380.14512629X-RAY DIFFRACTION100
1.6853-1.73490.18451370.13962606X-RAY DIFFRACTION100
1.7349-1.79080.1611370.14152599X-RAY DIFFRACTION100
1.7908-1.85480.16661380.14272609X-RAY DIFFRACTION100
1.8548-1.92910.17031380.14372626X-RAY DIFFRACTION100
1.9291-2.01690.16141390.14582638X-RAY DIFFRACTION100
2.0169-2.12320.16851370.14252607X-RAY DIFFRACTION100
2.1232-2.25620.17061390.13912640X-RAY DIFFRACTION100
2.2562-2.43040.17881380.13962619X-RAY DIFFRACTION99
2.4304-2.67490.12891390.14912654X-RAY DIFFRACTION100
2.6749-3.06170.16741410.15462667X-RAY DIFFRACTION100
3.0617-3.85650.16391410.14692692X-RAY DIFFRACTION100
3.8565-33.70220.15591470.14022789X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6550.4786-0.24411.3738-0.54850.45490.0087-0.00790.03930.05390.02060.1067-0.008-0.0515-0.03710.10010.00060.00220.12310.00110.0978-10.6792-28.352815.3131
20.37380.0632-0.06460.5697-0.12060.2816-0.01380.0183-0.005-0.03950.02960.06080.0308-0.0538-0.02080.1015-0.0034-0.00060.11430.0040.0944-10.2043-35.63313.6407
32.3649-0.5203-0.16832.03080.16612.0303-0.01890.12170.0435-0.1041-0.018-0.12470.04420.14370.0230.10820.00320.0090.12830.02680.1092-0.3093-12.1111-0.1713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 221 through 325 )
2X-RAY DIFFRACTION2chain 'A' and (resid 326 through 459 )
3X-RAY DIFFRACTION3chain 'A' and (resid 460 through 525 )

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