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- PDB-6gw1: GII.10 human norovirus protruding domain in complex with glycoche... -

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Basic information

Entry
Database: PDB / ID: 6gw1
TitleGII.10 human norovirus protruding domain in complex with glycochenodeoxycholate (GCDCA)
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Norovirus / GII.10 / P domain / GCDCA / 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
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)69,7846
Polymers68,8392
Non-polymers9454
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-8 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.850, 79.670, 87.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CHO / GLYCOCHENODEOXYCHOLIC ACID


Mass: 449.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H43NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
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: 0.97264 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97264 Å / Relative weight: 1
ReflectionResolution: 1.9→45.93 Å / Num. obs: 60120 / % possible obs: 99.38 % / Redundancy: 6.4 % / Biso Wilson estimate: 28.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06655 / Rpim(I) all: 0.02835 / Rrim(I) all: 0.07248 / Net I/σ(I): 16.89
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.6555 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 5732 / CC1/2: 0.8 / Rpim(I) all: 0.2838 / Rrim(I) all: 0.7159 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSVERSION Nov 1, 2016data reduction
XSCALEVERSION Nov 1, 2016data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONU

3onu


Resolution: 1.9→45.93 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.4
RfactorNum. reflection% reflection
Rfree0.1899 3006 5 %
Rwork0.1654 --
obs0.1667 60113 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 58 344 5110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054964
X-RAY DIFFRACTIONf_angle_d0.756837
X-RAY DIFFRACTIONf_dihedral_angle_d11.8262912
X-RAY DIFFRACTIONf_chiral_restr0.053780
X-RAY DIFFRACTIONf_plane_restr0.005895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92840.28871330.23232530X-RAY DIFFRACTION94
1.9284-1.96160.23231390.21912646X-RAY DIFFRACTION99
1.9616-1.99730.27181430.21312713X-RAY DIFFRACTION99
1.9973-2.03570.21921420.1972705X-RAY DIFFRACTION100
2.0357-2.07730.22661410.18672679X-RAY DIFFRACTION100
2.0773-2.12240.19661410.18082681X-RAY DIFFRACTION100
2.1224-2.17180.1961430.17522699X-RAY DIFFRACTION100
2.1718-2.22610.22021420.17392701X-RAY DIFFRACTION100
2.2261-2.28630.22841420.17192708X-RAY DIFFRACTION100
2.2863-2.35360.18671420.17082698X-RAY DIFFRACTION99
2.3536-2.42950.21021430.16772723X-RAY DIFFRACTION100
2.4295-2.51640.19291420.16822693X-RAY DIFFRACTION100
2.5164-2.61710.20841440.17772723X-RAY DIFFRACTION100
2.6171-2.73620.21231440.18242740X-RAY DIFFRACTION100
2.7362-2.88050.19851420.1822711X-RAY DIFFRACTION100
2.8805-3.06090.21081450.17532755X-RAY DIFFRACTION100
3.0609-3.29720.1961450.17292743X-RAY DIFFRACTION100
3.2972-3.62880.17571460.15962768X-RAY DIFFRACTION100
3.6288-4.15360.17441450.14472773X-RAY DIFFRACTION100
4.1536-5.2320.12151480.12332799X-RAY DIFFRACTION100
5.232-45.930.19921540.16622919X-RAY DIFFRACTION99
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)
12.0781-0.30120.98423.23220.05463.153-0.012-0.35230.15220.30680.0138-0.1362-0.11410.03340.01450.20520.0235-0.03320.2362-0.02020.1774-20.2769.4498-8.6278
24.53263.92551.96625.05631.33182.3196-0.0489-0.0796-0.23430.01610.1255-0.02730.06990.1033-0.10380.2030.0527-0.00130.18310.01420.2025-25.8736-4.0914-17.7067
33.85310.10820.40022.95340.82592.469-0.0579-0.1075-0.29310.23230.14430.10550.2788-0.0082-0.06250.3080.02280.00760.19370.07130.2712-33.5647-10.3844-16.9511
43.4675-0.17352.00932.3619-0.87164.81780.11060.1766-0.2997-0.13990.17060.08920.2408-0.0902-0.22420.1201-0.01680.02380.16540.03070.2274-38.1311-2.8035-25.506
51.77740.13250.8672.27030.64132.1776-0.0168-0.1968-0.27960.09330.08530.26230.1035-0.3051-0.06840.18050.00120.02160.26210.08240.256-40.615-3.5415-16.0082
61.77540.39680.12671.67520.03341.1814-0.048-0.4441-0.15960.39490.0985-0.21270.0636-0.0523-0.04810.28440.065-0.02210.3190.01550.1809-26.69782.9758-3.1555
75.692-1.1508-2.85994.62271.50446.63180.00220.0614-0.00170.00950.1037-0.3553-0.03760.185-0.09420.20020.0249-0.04550.2445-0.01880.2558-15.71586.7261-14.3843
84.2542-0.77020.56484.73690.56294.16140.0479-0.0990.3094-0.01350.0677-0.4874-0.18030.4175-0.13350.26070.0054-0.0830.317-0.10920.2792-11.351315.5821-4.4108
92.82230.11620.54252.02793.89868.0578-0.0557-0.25230.41240.32370.4177-0.68130.13020.8787-0.31570.2733-0.0029-0.09950.4581-0.17470.4911-5.19214.9372-2.2627
102.5734-0.9513-0.90071.53550.17291.25920.00820.06250.1571-0.08550.0165-0.0425-0.086-0.0287-0.03610.24060.012-0.02120.19260.00740.2153-27.273916.0947-30.9886
111.5202-0.0444-0.30851.0956-0.14120.9411-0.00510.0550.2047-0.05660.08940.1219-0.1291-0.1681-0.09310.19710.0298-0.01550.21350.02070.2092-36.636815.0624-31.3703
123.2763-0.1413-0.74652.41030.18921.6747-0.03690.137-0.2075-0.2096-0.0192-0.36320.07440.05680.02670.2306-0.00110.0570.1998-0.01390.3064-10.16634.9714-38.3902
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 354 )
5X-RAY DIFFRACTION5chain 'A' and (resid 355 through 409 )
6X-RAY DIFFRACTION6chain 'A' and (resid 410 through 455 )
7X-RAY DIFFRACTION7chain 'A' and (resid 456 through 472 )
8X-RAY DIFFRACTION8chain 'A' and (resid 473 through 521 )
9X-RAY DIFFRACTION9chain 'A' and (resid 522 through 538 )
10X-RAY DIFFRACTION10chain 'B' and (resid 225 through 332 )
11X-RAY DIFFRACTION11chain 'B' and (resid 333 through 455 )
12X-RAY DIFFRACTION12chain 'B' and (resid 456 through 538 )

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