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- PDB-6qw5: Structure and function of the toscana virus cap snatching endonuclease -

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Basic information

Entry
Database: PDB / ID: 6qw5
TitleStructure and function of the toscana virus cap snatching endonuclease
ComponentsRNA-dependent RNA polymerase
KeywordsHYDROLASE / Cap snatching endonuclease of Toscana virus at the N-term of the L protein.
Function / homology
Function and homology information


RNA-templated viral transcription / nucleoside binding / negative stranded viral RNA replication / host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase ...RNA-templated viral transcription / nucleoside binding / negative stranded viral RNA replication / host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase, phlebovirus / RNA-directed RNA polymerase L, PA-C-like domain / RNA-directed RNA polymerase L, PA-C-like domain / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
: / 2-4-DIOXO-4-PHENYLBUTANOIC ACID / RNA-directed RNA polymerase L / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesToscana virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.988 Å
AuthorsReguera, J. / Jones, R. / Bragagniolo, G. / Lessoued, S. / Mate, M.
Funding support France, 1items
OrganizationGrant numberCountry
France
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structure and function of the Toscana virus cap-snatching endonuclease.
Authors: Jones, R. / Lessoued, S. / Meier, K. / Devignot, S. / Barata-Garcia, S. / Mate, M. / Bragagnolo, G. / Weber, F. / Rosenthal, M. / Reguera, J.
History
DepositionMar 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,77312
Polymers47,7852
Non-polymers98810
Water5,675315
1
A: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3876
Polymers23,8921
Non-polymers4945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3876
Polymers23,8921
Non-polymers4945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.957, 106.209, 58.623
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-553-

HOH

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Components

#1: Protein RNA-dependent RNA polymerase / cap-snatching endonuclease


Mass: 23892.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 2,4-dioxo-4-phenylbutanoic acid / Source: (gene. exp.) Toscana virus
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: S4ZA26, UniProt: P37800*PLUS
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XI7 / 2-4-DIOXO-4-PHENYLBUTANOIC ACID


Mass: 192.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 3.46 Å3/Da / Density % sol: 64.42 % / Description: Thick plates
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0,1M Hepes pH 7,5 0,75 M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.98→47.1 Å / Num. all: 44372 / Num. obs: 36170 / % possible obs: 99 % / Redundancy: 10.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.056 / Rrim(I) all: 0.185 / Net I/σ(I): 0.1
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6019 / CC1/2: 0.818 / Rpim(I) all: 0.376 / Rrim(I) all: 0.871 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.988→47.099 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 2138 5.16 %RANDOM
Rwork0.2032 ---
obs0.2052 41468 93.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.988→47.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 52 315 3415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073180
X-RAY DIFFRACTIONf_angle_d0.7474327
X-RAY DIFFRACTIONf_dihedral_angle_d2.4032571
X-RAY DIFFRACTIONf_chiral_restr0.055509
X-RAY DIFFRACTIONf_plane_restr0.005555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9881-2.03440.4069850.33611811X-RAY DIFFRACTION64
2.0344-2.08520.32061270.26882201X-RAY DIFFRACTION79
2.0852-2.14160.29481340.23422266X-RAY DIFFRACTION82
2.1416-2.20460.28361280.21942351X-RAY DIFFRACTION85
2.2046-2.27580.26431340.21462477X-RAY DIFFRACTION89
2.2758-2.35710.24651560.21892652X-RAY DIFFRACTION95
2.3571-2.45150.2571520.21692771X-RAY DIFFRACTION99
2.4515-2.56310.20871470.20792787X-RAY DIFFRACTION100
2.5631-2.69820.24851520.19692805X-RAY DIFFRACTION100
2.6982-2.86720.21531460.19032814X-RAY DIFFRACTION100
2.8672-3.08860.24011690.17892806X-RAY DIFFRACTION100
3.0886-3.39930.20081580.18222810X-RAY DIFFRACTION100
3.3993-3.8910.2071560.17452865X-RAY DIFFRACTION100
3.891-4.90140.21141330.18082910X-RAY DIFFRACTION100
4.9014-47.1120.29341610.23623004X-RAY DIFFRACTION100

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