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- PDB-5cyr: Crystal structure of Thosea asigna virus RNA-dependent RNA polyme... -

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Basic information

Entry
Database: PDB / ID: 5cyr
TitleCrystal structure of Thosea asigna virus RNA-dependent RNA polymerase (RdRP) complexed with ATP and ssRNA
ComponentsRNA-dependent RNA polymerase
KeywordsTRANSCRIPTION / RdRP / complex / ATP / ssRNA
Function / homologyRNA-dependent RNA polymerase activity / DNA/RNA polymerase superfamily / ATP binding / metal ion binding / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / RNA-dependent RNA polymerase
Function and homology information
Biological speciesThosea asigna virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.504 Å
AuthorsFerrero, D.S. / Buxaderas, M. / Rodriguez, J.F. / Verdaguer, N.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2011-24333 Spain
Spanish Ministry of Economy and CompetitivenessAGL2011-24758 Spain
CitationJournal: Plos Pathog. / Year: 2015
Title: The Structure of the RNA-Dependent RNA Polymerase of a Permutotetravirus Suggests a Link between Primer-Dependent and Primer-Independent Polymerases.
Authors: Ferrero, D.S. / Buxaderas, M. / Rodriguez, J.F. / Verdaguer, N.
History
DepositionJul 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Advisory / Author supporting evidence
Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RNA-dependent RNA polymerase
A: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,18410
Polymers159,0812
Non-polymers1,1038
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-101 kcal/mol
Surface area53350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.513, 158.339, 217.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein RNA-dependent RNA polymerase


Mass: 79540.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thosea asigna virus / Gene: RdRp / Plasmid: pFastBac1-HM / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6A562
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, Lithium sulfate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.504→48.4 Å / Num. obs: 27974 / % possible obs: 89.61 % / Redundancy: 8.1 % / Rsym value: 0.15 / Net I/σ(I): 5.57
Reflection shellResolution: 3.504→3.629 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.3 / % possible all: 75.92

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XHI

4xhi


Resolution: 3.504→47.599 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2956 1412 5.05 %
Rwork0.2517 --
obs0.2539 27936 89.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.504→47.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10466 0 62 0 10528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410744
X-RAY DIFFRACTIONf_angle_d0.89414567
X-RAY DIFFRACTIONf_dihedral_angle_d14.9973985
X-RAY DIFFRACTIONf_chiral_restr0.0331594
X-RAY DIFFRACTIONf_plane_restr0.0031880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.504-3.62920.43091170.38132219X-RAY DIFFRACTION76
3.6292-3.77440.49121260.42282253X-RAY DIFFRACTION77
3.7744-3.94610.4222950.3641725X-RAY DIFFRACTION59
3.9461-4.15410.29841570.23332814X-RAY DIFFRACTION97
4.1541-4.41420.24541460.20742926X-RAY DIFFRACTION98
4.4142-4.75470.23221620.19482911X-RAY DIFFRACTION98
4.7547-5.23270.23311350.2022891X-RAY DIFFRACTION98
5.2327-5.98860.25411620.22032893X-RAY DIFFRACTION98
5.9886-7.54010.26941570.22872914X-RAY DIFFRACTION97
7.5401-47.60380.23961550.19932978X-RAY DIFFRACTION95

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