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- PDB-7oma: Thosea asigna virus RdRP domain elongation complex -

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Basic information

Entry
Database: PDB / ID: 7oma
TitleThosea asigna virus RdRP domain elongation complex
Components
  • RNA (5'-R(P*AP*AP*AP*UP*UP*UP*U)-3')
  • RNA (5'-R(P*CP*AP*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
PYROPHOSPHATE 2- / RNA / RNA-dependent RNA polymerase
Similarity search - Component
Biological speciesThosea asigna virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_scat_Cromer_Mann_a5 / _atom_type.pdbx_scat_Cromer_Mann_b5 ..._atom_type.pdbx_scat_Cromer_Mann_a5 / _atom_type.pdbx_scat_Cromer_Mann_b5 / _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
C: RNA-dependent RNA polymerase
D: RNA-dependent RNA polymerase
E: RNA (5'-R(P*AP*AP*AP*UP*UP*UP*U)-3')
F: RNA (5'-R(P*CP*AP*AP*AP*AP*UP*UP*U)-3')
G: RNA (5'-R(P*AP*AP*AP*UP*UP*UP*U)-3')
H: RNA (5'-R(P*CP*AP*AP*AP*AP*UP*UP*U)-3')
I: RNA (5'-R(P*AP*AP*AP*UP*UP*UP*U)-3')
J: RNA (5'-R(P*CP*AP*AP*AP*AP*UP*UP*U)-3')
L: RNA (5'-R(P*AP*AP*AP*UP*UP*UP*U)-3')
K: RNA (5'-R(P*CP*AP*AP*AP*AP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,28120
Polymers329,63112
Non-polymers6498
Water00
1
B: RNA-dependent RNA polymerase
A: RNA-dependent RNA polymerase
E: RNA (5'-R(P*AP*AP*AP*UP*UP*UP*U)-3')
F: RNA (5'-R(P*CP*AP*AP*AP*AP*UP*UP*U)-3')
G: RNA (5'-R(P*AP*AP*AP*UP*UP*UP*U)-3')
H: RNA (5'-R(P*CP*AP*AP*AP*AP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,24111
Polymers164,8166
Non-polymers4255
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14800 Å2
ΔGint-130 kcal/mol
Surface area52970 Å2
MethodPISA
2
C: RNA-dependent RNA polymerase
D: RNA-dependent RNA polymerase
I: RNA (5'-R(P*AP*AP*AP*UP*UP*UP*U)-3')
J: RNA (5'-R(P*CP*AP*AP*AP*AP*UP*UP*U)-3')
L: RNA (5'-R(P*AP*AP*AP*UP*UP*UP*U)-3')
K: RNA (5'-R(P*CP*AP*AP*AP*AP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,0409
Polymers164,8166
Non-polymers2253
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14610 Å2
ΔGint-121 kcal/mol
Surface area52660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.794, 207.305, 115.980
Angle α, β, γ (deg.)90.000, 91.101, 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.: 4
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*UP*U)-3')


Mass: 2801.710 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: RNA chain
RNA (5'-R(P*CP*AP*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)
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate pH4.6, 0.22M (NH4)SO4, 28% PEG2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→67.78 Å / Num. obs: 57906 / % possible obs: 99.89 % / Redundancy: 6.9 % / Biso Wilson estimate: 57.14 Å2 / CC1/2: 0.951 / Rmerge(I) obs: 0.3841 / Net I/σ(I): 6.79
Reflection shellResolution: 3.1→3.211 Å / Rmerge(I) obs: 2.066 / Mean I/σ(I) obs: 1.22 / Num. unique obs: 5770 / CC1/2: 0.391 / Rpim(I) all: 0.8418 / % possible all: 99.84

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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: 3.1→67.78 Å / SU ML: 0.425 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6409
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2579 2836 4.9 %
Rwork0.2309 55013 -
obs0.2322 57849 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.06 Å2
Refinement stepCycle: LAST / Resolution: 3.1→67.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19942 1256 32 0 21230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005721794
X-RAY DIFFRACTIONf_angle_d0.85829765
X-RAY DIFFRACTIONf_chiral_restr0.04663336
X-RAY DIFFRACTIONf_plane_restr0.00623612
X-RAY DIFFRACTIONf_dihedral_angle_d17.62188276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.150.33791470.34632720X-RAY DIFFRACTION99.83
3.15-3.210.35041700.32822726X-RAY DIFFRACTION99.86
3.21-3.270.37411390.33032711X-RAY DIFFRACTION99.82
3.27-3.340.34211310.30822766X-RAY DIFFRACTION99.9
3.34-3.410.29771310.29592799X-RAY DIFFRACTION99.97
3.41-3.490.32261580.27022679X-RAY DIFFRACTION99.86
3.49-3.580.33781430.26312784X-RAY DIFFRACTION100
3.58-3.680.28551420.25112701X-RAY DIFFRACTION99.93
3.68-3.780.26111370.23932777X-RAY DIFFRACTION99.97
3.78-3.910.2761350.22812726X-RAY DIFFRACTION99.97
3.91-4.050.24271250.22722767X-RAY DIFFRACTION99.79
4.05-4.210.24891160.21282802X-RAY DIFFRACTION99.97
4.21-4.40.22031400.19082735X-RAY DIFFRACTION100
4.4-4.630.17831530.17922736X-RAY DIFFRACTION99.93
4.63-4.920.22291630.18552737X-RAY DIFFRACTION99.97
4.92-5.30.19391380.19582764X-RAY DIFFRACTION99.93
5.3-5.830.23511700.21152707X-RAY DIFFRACTION99.93
5.83-6.680.28551360.22822785X-RAY DIFFRACTION99.9
6.68-8.410.25521260.21592801X-RAY DIFFRACTION99.9
8.41-67.780.22181360.20722790X-RAY DIFFRACTION99.52

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