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- PDB-6gw2: GII.10 human norovirus protruding domain in complex with tauroche... -

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Basic information

Entry
Database: PDB / ID: 6gw2
TitleGII.10 human norovirus protruding domain in complex with taurochenodeoxycholate (TCDCA)
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Norovirus / GII.10 / 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
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1499
Polymers68,8392
Non-polymers1,3107
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint0 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.830, 87.910, 108.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-756-

HOH

21A-793-

HOH

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Components

#1: Protein Capsid protein


Mass: 34419.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5F4T5
#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.: 2 / Source method: obtained synthetically / Formula: C26H45NO6S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0,1M Magnesium acetate tetrahydrate 0,1M Sodium citrate pH 5,8 14% w/v PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97372 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97372 Å / Relative weight: 1
ReflectionResolution: 2.05→46.12 Å / Num. obs: 48586 / % possible obs: 99.65 % / Redundancy: 6.3 % / Biso Wilson estimate: 34.59 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09804 / Rpim(I) all: 0.04248 / Rrim(I) all: 0.107 / Net I/σ(I): 11.02
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.6477 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 4669 / CC1/2: 0.793 / Rpim(I) all: 0.2783 / Rrim(I) all: 0.7062 / % possible all: 97.33

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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: 3ONU

3onu


Resolution: 2.05→46.118 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.01
RfactorNum. reflection% reflection
Rfree0.2063 2430 5 %
Rwork0.1695 --
obs0.1713 48564 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→46.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4694 0 88 273 5055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054921
X-RAY DIFFRACTIONf_angle_d0.6856758
X-RAY DIFFRACTIONf_dihedral_angle_d12.0182857
X-RAY DIFFRACTIONf_chiral_restr0.049771
X-RAY DIFFRACTIONf_plane_restr0.004875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0471-2.08890.34181350.25672555X-RAY DIFFRACTION95
2.0889-2.13430.22921390.22232654X-RAY DIFFRACTION100
2.1343-2.1840.22131410.19952681X-RAY DIFFRACTION100
2.184-2.23860.23961430.1962698X-RAY DIFFRACTION100
2.2386-2.29910.21611420.18582699X-RAY DIFFRACTION100
2.2991-2.36680.23361420.18162703X-RAY DIFFRACTION100
2.3668-2.44310.25731420.18682693X-RAY DIFFRACTION100
2.4431-2.53050.22231410.17842687X-RAY DIFFRACTION100
2.5305-2.63180.27641420.18752703X-RAY DIFFRACTION100
2.6318-2.75150.21571440.18782719X-RAY DIFFRACTION100
2.7515-2.89660.2151410.18152695X-RAY DIFFRACTION100
2.8966-3.0780.21181440.17862734X-RAY DIFFRACTION100
3.078-3.31560.2381430.18042715X-RAY DIFFRACTION100
3.3156-3.64920.22861450.16372755X-RAY DIFFRACTION100
3.6492-4.17690.17071450.14542749X-RAY DIFFRACTION100
4.1769-5.26130.15471470.13312776X-RAY DIFFRACTION100
5.2613-46.12930.18471540.16822918X-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)
13.2152-0.52360.03792.22461.07411.37910.03010.1604-0.214-0.12030.012-0.0550.62470.2038-0.03610.37390.0447-0.030.2342-0.01380.27689.6506-35.2793-33.6598
23.7822-0.7752-2.35331.87211.14195.9770.1393-0.00780.0255-0.1261-0.10770.21690.0949-0.3758-0.00880.1904-0.0283-0.02860.29990.04150.3012-3.923-26.0914-27.7863
33.0505-1.30890.3812.22821.16251.2575-0.015-0.2751-0.24850.0085-0.11980.28480.1789-0.3915-0.00720.2626-0.1102-0.01250.44940.04870.3955-10.238-27.035-20.4478
41.725-0.05860.09091.07150.06092.88180.1476-0.0591-0.19310.0748-0.04790.13750.5142-0.4311-0.01670.2923-0.0825-0.04320.27040.04330.2550.2891-31.0189-21.7014
54.1938-0.91360.18074.33350.08421.28860.08950.6512-0.2309-0.3153-0.1513-0.09730.56890.46350.12920.62130.2101-0.0220.454-0.08880.327915.8883-39.6651-42.8247
61.3346-2.1822-0.02384.77190.83830.51330.21050.5593-0.3596-0.6197-0.1137-0.27640.70070.6299-0.27360.71410.22650.00170.4562-0.09770.302714.8702-41.8443-48.7645
71.89050.15061.04411.0364-1.36594.07580.05120.08580.11380.0608-0.0861-0.1445-0.10340.38730.03950.2328-0.01050.00020.2406-0.01520.328216.2533-13.2507-26.8805
80.8776-0.50910.58434.0225-2.43232.94840.2978-0.1133-0.063-0.0142-0.3867-0.2820.43640.36140.09850.3280.0053-0.04850.31710.01610.340516.6497-25.701-13.8805
91.57660.28950.18291.3857-0.82623.00260.1598-0.15660.21350.2901-0.1318-0.1238-0.49620.35580.02690.3116-0.0561-0.01430.269-0.02170.306614.9568-9.5805-18.4745
102.3228-0.47250.18881.9466-0.83863.48420.08230.38380.3069-0.05180.09430.1843-0.423-0.2859-0.0890.26070.04810.02770.37830.13030.3495.0393-5.373-43.7944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 226 through 266 )
2X-RAY DIFFRACTION2chain 'A' and (resid 267 through 294 )
3X-RAY DIFFRACTION3chain 'A' and (resid 295 through 327 )
4X-RAY DIFFRACTION4chain 'A' and (resid 328 through 472 )
5X-RAY DIFFRACTION5chain 'A' and (resid 473 through 521 )
6X-RAY DIFFRACTION6chain 'A' and (resid 522 through 538 )
7X-RAY DIFFRACTION7chain 'B' and (resid 225 through 327 )
8X-RAY DIFFRACTION8chain 'B' and (resid 328 through 354 )
9X-RAY DIFFRACTION9chain 'B' and (resid 355 through 455 )
10X-RAY DIFFRACTION10chain 'B' and (resid 456 through 538 )

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