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- PDB-7om6: Thosea asigna virus RdRP domain in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 7om6
TitleThosea asigna virus RdRP domain in complex with RNA
Components
  • RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
  • RNA-dependent RNA polymerase
KeywordsVIRAL PROTEIN / RdRP / polymerase
Function / homology
Function and homology information


RNA-directed RNA polymerase activity / ATP binding / metal ion binding
Similarity search - Function
: / : / Permutotetravirus RNA-dependent RNA polymerase palm domain / Permutotetravirus RNA-dependent RNA polymerase thumb domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / RNA / RNA-dependent RNA polymerase
Similarity search - Component
Biological speciesThosea asigna virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsFerrero, D.S. / Falqui, M. / Verdaguer, N.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBIO2017-83906-P Spain
Spanish National Research Council2020AEP121 Spain
CitationJournal: Viruses / Year: 2021
Title: Snapshots of a Non-Canonical RdRP in Action.
Authors: Ferrero, D.S. / Falqui, M. / Verdaguer, N.
History
DepositionMay 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: RNA-dependent RNA polymerase
B: RNA-dependent RNA polymerase
C: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
D: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
E: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
F: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,4168
Polymers164,2036
Non-polymers2122
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14340 Å2
ΔGint-69 kcal/mol
Surface area53260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.636, 204.028, 70.076
Angle α, β, γ (deg.)90.000, 97.190, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein RNA-dependent RNA polymerase


Mass: 77110.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thosea asigna virus / Gene: RdRp / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6A562
#2: RNA chain
RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')


Mass: 2495.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.84 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate pH4.6, 0.25M (NH4)SO4, 26% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.18→49.3 Å / Num. obs: 94404 / % possible obs: 99.03 % / Redundancy: 3.5 % / Biso Wilson estimate: 41.68 Å2 / CC1/2: 0.997 / Net I/σ(I): 14.15
Reflection shellResolution: 2.18→2.26 Å / Num. unique obs: 9474 / CC1/2: 0.737

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XHI

4xhi


Resolution: 2.18→49.3 Å / SU ML: 0.2823 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.3438
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2412 4523 4.81 %
Rwork0.2287 89431 -
obs0.2293 93954 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.79 Å2
Refinement stepCycle: LAST / Resolution: 2.18→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10013 588 14 555 11170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011710895
X-RAY DIFFRACTIONf_angle_d1.641614861
X-RAY DIFFRACTIONf_chiral_restr0.08911665
X-RAY DIFFRACTIONf_plane_restr0.00621811
X-RAY DIFFRACTIONf_dihedral_angle_d16.51914133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.20.35081500.37162954X-RAY DIFFRACTION98.35
2.2-2.230.36181220.35482965X-RAY DIFFRACTION98.82
2.23-2.260.33661550.33963014X-RAY DIFFRACTION98.51
2.26-2.290.39551430.31652911X-RAY DIFFRACTION98.8
2.29-2.320.36181590.32382955X-RAY DIFFRACTION98.7
2.32-2.350.30361380.32863034X-RAY DIFFRACTION98.51
2.35-2.380.36141350.30852930X-RAY DIFFRACTION98.74
2.38-2.420.31141460.30673009X-RAY DIFFRACTION98.72
2.42-2.460.30061410.31042935X-RAY DIFFRACTION98.75
2.46-2.50.33071410.28992971X-RAY DIFFRACTION97.43
2.5-2.540.26331630.29142919X-RAY DIFFRACTION98.47
2.54-2.580.30091600.29222963X-RAY DIFFRACTION99.27
2.58-2.630.2931560.28222980X-RAY DIFFRACTION99.46
2.63-2.690.27931810.28192977X-RAY DIFFRACTION99.5
2.69-2.750.26861650.27912982X-RAY DIFFRACTION99.27
2.75-2.810.32791560.28872990X-RAY DIFFRACTION99.71
2.81-2.880.28441340.28812983X-RAY DIFFRACTION99.46
2.88-2.960.31361710.26742975X-RAY DIFFRACTION99.15
2.96-3.050.21911440.27162958X-RAY DIFFRACTION98.41
3.05-3.140.25061350.24232990X-RAY DIFFRACTION98.55
3.14-3.260.26851480.24413008X-RAY DIFFRACTION99.81
3.26-3.390.26041520.23822983X-RAY DIFFRACTION99.62
3.39-3.540.24621550.23173010X-RAY DIFFRACTION99.5
3.54-3.730.22461620.20862988X-RAY DIFFRACTION99.78
3.73-3.960.22551300.19662995X-RAY DIFFRACTION99.27
3.96-4.270.20211380.17833015X-RAY DIFFRACTION98.72
4.27-4.70.181770.17162998X-RAY DIFFRACTION99.78
4.7-5.370.20021470.17883016X-RAY DIFFRACTION99.72
5.37-6.770.17671540.19692988X-RAY DIFFRACTION99.21
6.77-49.30.18911650.16963035X-RAY DIFFRACTION99.5

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