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- PDB-6qwt: Sicinivirus 3Dpol RNA dependent RNA polymerase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6qwt
TitleSicinivirus 3Dpol RNA dependent RNA polymerase
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / 3Dpol / RdRp
Function / homology
Function and homology information


RNA-protein covalent cross-linking / : / cysteine-type peptidase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity ...RNA-protein covalent cross-linking / : / cysteine-type peptidase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding
Similarity search - Function
Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Reverse transcriptase/Diguanylate cyclase domain / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Reverse transcriptase/Diguanylate cyclase domain / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Alpha-Beta Plaits / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesChicken sicinivirus JSY
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsDubankova, A. / Boura, E.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000729 Czech Republic
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Structures of kobuviral and siciniviral polymerases reveal conserved mechanism of picornaviral polymerase activation.
Authors: Dubankova, A. / Horova, V. / Klima, M. / Boura, E.
History
DepositionMar 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)52,9181
Polymers52,9181
Non-polymers00
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.509, 92.509, 161.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-698-

HOH

21A-799-

HOH

31A-848-

HOH

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Components

#1: Protein Genome polyprotein


Mass: 52917.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chicken sicinivirus JSY / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0QLC4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 12,5 % PEG 1000, 12,5 % PEG 3350, 12,5 % (RS)-2-methyl-2,4-pentanediol, 0,2 M 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M ...Details: 12,5 % PEG 1000, 12,5 % PEG 3350, 12,5 % (RS)-2-methyl-2,4-pentanediol, 0,2 M 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol and 0,1 M MES/Imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→46.62 Å / Num. obs: 31996 / % possible obs: 99.93 % / Redundancy: 14 % / Net I/σ(I): 13.4
Reflection shellResolution: 2.3→2.382 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Cootmodel building
PHENIXphasing
MxCuBEdata collection
RefinementResolution: 2.3→46.62 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.29
RfactorNum. reflection% reflection
Rfree0.2239 1600 5 %
Rwork0.1899 --
obs0.1917 31991 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 0 484 4196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033836
X-RAY DIFFRACTIONf_angle_d0.5785248
X-RAY DIFFRACTIONf_dihedral_angle_d22.1981366
X-RAY DIFFRACTIONf_chiral_restr0.044566
X-RAY DIFFRACTIONf_plane_restr0.005679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2998-2.37410.3031410.25672684X-RAY DIFFRACTION99
2.3741-2.45890.27091430.23782718X-RAY DIFFRACTION100
2.4589-2.55740.27761420.22252702X-RAY DIFFRACTION100
2.5574-2.67370.26391440.22312718X-RAY DIFFRACTION100
2.6737-2.81470.25021430.20642725X-RAY DIFFRACTION100
2.8147-2.9910.26161440.21242740X-RAY DIFFRACTION100
2.991-3.22190.24261440.20152733X-RAY DIFFRACTION100
3.2219-3.5460.2281460.18562772X-RAY DIFFRACTION100
3.546-4.05890.17191470.16162788X-RAY DIFFRACTION100
4.0589-5.11280.17741480.1492821X-RAY DIFFRACTION100
5.1128-46.62910.21681580.18762990X-RAY DIFFRACTION100

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