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- PDB-7om7: Thosea asigna virus RdRP domain in complex with RNA and nucleotid... -

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Basic information

Entry
Database: PDB / ID: 7om7
TitleThosea asigna virus RdRP domain in complex with RNA and nucleotide UMPNPP
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
Chem-2KH / : / 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: 2.4 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-dependent RNA polymerase
D: RNA-dependent RNA polymerase
E: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
F: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
G: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
H: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
I: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
J: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
K: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
L: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,53416
Polymers328,40712
Non-polymers1,1274
Water9,440524
1
A: RNA-dependent RNA polymerase
B: RNA-dependent RNA polymerase
E: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
F: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
G: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
H: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,2259
Polymers164,2036
Non-polymers1,0213
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13960 Å2
ΔGint-105 kcal/mol
Surface area52420 Å2
MethodPISA
2
C: RNA-dependent RNA polymerase
D: RNA-dependent RNA polymerase
I: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
J: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
K: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
L: RNA (5'-R(P*AP*AP*AP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,3107
Polymers164,2036
Non-polymers1061
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13680 Å2
ΔGint-87 kcal/mol
Surface area53760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.480, 206.266, 115.590
Angle α, β, γ (deg.)90.000, 90.745, 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

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Protein / RNA chain , 2 types, 12 molecules ABCDEFGHIJKL

#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*U)-3')


Mass: 2495.545 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 4 types, 528 molecules

#3: Chemical ChemComp-2KH / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.78 %
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: Mar 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→59.09 Å / Num. obs: 122219 / % possible obs: 99.44 % / Redundancy: 12 % / Biso Wilson estimate: 50.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1305 / Rpim(I) all: 0.0389 / Rrim(I) all: 0.1363 / Net I/σ(I): 17.25
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 1.717 / Num. unique obs: 12216 / CC1/2: 0.725 / Rpim(I) all: 0.5098 / Rrim(I) all: 1.792 / % possible all: 99.58

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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: 2.4→59.09 Å / SU ML: 0.3188 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6247
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2155 6025 4.93 %
Rwork0.2147 116194 -
obs0.2147 122219 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.38 Å2
Refinement stepCycle: LAST / Resolution: 2.4→59.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19957 1198 66 524 21745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010221788
X-RAY DIFFRACTIONf_angle_d1.391929750
X-RAY DIFFRACTIONf_chiral_restr0.08313338
X-RAY DIFFRACTIONf_plane_restr0.00533609
X-RAY DIFFRACTIONf_dihedral_angle_d14.69698249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.35041960.35393831X-RAY DIFFRACTION99.43
2.43-2.460.32441950.34643886X-RAY DIFFRACTION99.59
2.46-2.490.33731850.33483905X-RAY DIFFRACTION99.71
2.49-2.520.34222130.32263895X-RAY DIFFRACTION99.76
2.52-2.550.31012110.31673813X-RAY DIFFRACTION99.58
2.55-2.590.32831790.31623911X-RAY DIFFRACTION99.68
2.59-2.620.31331940.30093860X-RAY DIFFRACTION99.73
2.62-2.660.29281920.30033862X-RAY DIFFRACTION99.53
2.66-2.70.32982070.31573909X-RAY DIFFRACTION99.47
2.7-2.750.3362270.32333815X-RAY DIFFRACTION99.26
2.75-2.790.28362220.30693832X-RAY DIFFRACTION99.41
2.79-2.850.29072100.2873815X-RAY DIFFRACTION99.06
2.85-2.90.30452030.27163903X-RAY DIFFRACTION99.3
2.9-2.960.26732110.2653818X-RAY DIFFRACTION98.8
2.96-3.020.26092010.26643819X-RAY DIFFRACTION98.94
3.02-3.090.25992110.25383863X-RAY DIFFRACTION99.08
3.09-3.170.23871670.24513876X-RAY DIFFRACTION99.07
3.17-3.260.26541770.24493884X-RAY DIFFRACTION99.24
3.26-3.350.24241930.24673901X-RAY DIFFRACTION99.49
3.35-3.460.23722070.23563859X-RAY DIFFRACTION99.36
3.46-3.580.21331880.21263883X-RAY DIFFRACTION99.51
3.58-3.730.21181990.19523918X-RAY DIFFRACTION99.37
3.73-3.90.1832260.19163818X-RAY DIFFRACTION99.68
3.9-4.10.17841800.18523903X-RAY DIFFRACTION99.88
4.1-4.360.16851910.16763905X-RAY DIFFRACTION99.85
4.36-4.70.15672300.1573885X-RAY DIFFRACTION99.88
4.7-5.170.16872230.1693898X-RAY DIFFRACTION99.69
5.17-5.920.1812330.17993827X-RAY DIFFRACTION99.41
5.92-7.450.18361730.18233955X-RAY DIFFRACTION99.3
7.45-59.090.16271810.16183945X-RAY DIFFRACTION99.21

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