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- PDB-6gw4: GII.22 human norovirus protruding domain in complex with glycoche... -

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Basic information

Entry
Database: PDB / ID: 6gw4
TitleGII.22 human norovirus protruding domain in complex with glycochenodeoxycholate (GCDCA)
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Norovirus / GII.19 / P domain / GCDCA / HBGA
Function / homology
Function and homology information


Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / 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 ...Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / 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-like virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.295 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
Revision 1.4Jul 31, 2024Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4446
Polymers33,7461
Non-polymers6985
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint7 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.240, 81.240, 223.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-736-

HOH

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Components

#1: Protein Capsid protein


Mass: 33746.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk-like virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0ZNP3
#2: Chemical ChemComp-CHO / GLYCOCHENODEOXYCHOLIC ACID


Mass: 449.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H43NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate 0.1 M Sodium acetate pH 4.6 30%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 1.54→59.86 Å / Num. obs: 44206 / % possible obs: 99.36 % / Redundancy: 13.7 % / Biso Wilson estimate: 16.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05719 / Rpim(I) all: 0.01599 / Rrim(I) all: 0.05943 / Net I/σ(I): 27.7
Reflection shellResolution: 1.54→1.59 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.6674 / Mean I/σ(I) obs: 3.57 / Num. unique obs: 4133 / CC1/2: 0.938 / Rpim(I) all: 0.1883 / Rrim(I) all: 0.694 / % possible all: 94.22

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSVERSION Nov 11, 2017data reduction
XSCALEVERSION Nov 11, 2017data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONU

3onu


Resolution: 2.295→43.804 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.42
RfactorNum. reflection% reflection
Rfree0.2137 1022 5.01 %
Rwork0.175 --
obs0.177 20419 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.295→43.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 48 98 2474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032447
X-RAY DIFFRACTIONf_angle_d0.5883348
X-RAY DIFFRACTIONf_dihedral_angle_d10.8031425
X-RAY DIFFRACTIONf_chiral_restr0.048367
X-RAY DIFFRACTIONf_plane_restr0.005442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2953-2.41640.25221410.19572677X-RAY DIFFRACTION99
2.4164-2.56770.28081430.19222711X-RAY DIFFRACTION100
2.5677-2.7660.2271420.19392704X-RAY DIFFRACTION100
2.766-3.04420.23861440.19792734X-RAY DIFFRACTION100
3.0442-3.48460.24351460.18812757X-RAY DIFFRACTION100
3.4846-4.38960.2011470.16032811X-RAY DIFFRACTION100
4.3896-43.81220.17581590.15823003X-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)
10.78470.3807-0.34170.8993-0.55360.95790.0531-0.0248-0.02130.1122-0.079-0.0123-0.1383-0.14510.04210.3450.02690.03010.2425-0.01480.29237.0944-19.3636-9.598
21.08640.3501-0.78980.3873-0.2120.6463-0.1780.42630.46830.1420.2332-0.0228-0.3197-0.10320.06140.43420.0547-0.03640.24030.03430.388441.543-1.5214-17.6603
30.45940.16070.42441.1889-0.62411.13910.0632-0.06420.0930.2962-0.111-0.0013-0.42220.07830.01440.36930.00960.01440.2215-0.00960.29746.9248-8.8921-11.8775
41.47881.0261-0.32882.3621-1.16523.32690.0645-0.0578-0.11920.1493-0.04370.06890-0.2887-0.0740.2710.00250.03930.26970.00890.296230.8795-31.0527-2.0422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 225 through 293 )
2X-RAY DIFFRACTION2chain 'A' and (resid 294 through 326 )
3X-RAY DIFFRACTION3chain 'A' and (resid 327 through 448 )
4X-RAY DIFFRACTION4chain 'A' and (resid 449 through 531 )

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