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- PDB-6qw0: Structure and function of toscana virus cap snatching endonucleases -

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Basic information

Entry
Database: PDB / ID: 6qw0
TitleStructure and function of toscana virus cap snatching endonucleases
ComponentsRNA-dependent RNA polymerase
KeywordsHYDROLASE / Cap snatching endonuclease / Toscana virus / 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 / nucleotide binding / RNA-directed RNA polymerase activity / 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
MANGANESE (III) ION / RNA-directed RNA polymerase L / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesToscana virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsReguera, J. / Jones, R. / Bragagniolo, G. / Lessoued, S. / Mate, M.
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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,57312
Polymers47,7852
Non-polymers78810
Water6,557364
1
A: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3837
Polymers23,8921
Non-polymers4906
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1905
Polymers23,8921
Non-polymers2984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.847, 107.848, 58.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein RNA-dependent RNA polymerase


Mass: 23892.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toscana virus
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: S4ZA26, UniProt: P37800*PLUS
#2: Chemical
ChemComp-MN3 / MANGANESE (III) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.35 Å3/Da / Density % sol: 63.28 %
Crystal growTemperature: 293 K / Method: counter-diffusion / Details: 0.1 M 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: 0.97857 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.5→47.553 Å / Num. obs: 99878 / % possible obs: 97.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.042 / Net I/σ(I): 11.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.4 % / Rmerge(I) obs: 2.497 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4745 / CC1/2: 0.318 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QW5

6qw5


Resolution: 1.5→47.553 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.35
RfactorNum. reflection% reflection
Rfree0.2356 4959 4.97 %
Rwork0.2085 --
obs0.2098 99758 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→47.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 36 365 3386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063148
X-RAY DIFFRACTIONf_angle_d0.7394285
X-RAY DIFFRACTIONf_dihedral_angle_d2.5382547
X-RAY DIFFRACTIONf_chiral_restr0.056499
X-RAY DIFFRACTIONf_plane_restr0.006552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.44091370.40462989X-RAY DIFFRACTION93
1.517-1.53490.41961490.40873053X-RAY DIFFRACTION95
1.5349-1.55360.38881610.37863127X-RAY DIFFRACTION97
1.5536-1.57330.40221580.38523106X-RAY DIFFRACTION96
1.5733-1.5940.41171510.40693077X-RAY DIFFRACTION97
1.594-1.61580.4111870.37253079X-RAY DIFFRACTION96
1.6158-1.63890.30911560.35053076X-RAY DIFFRACTION96
1.6389-1.66340.34151670.31763096X-RAY DIFFRACTION97
1.6634-1.68940.33831620.2943109X-RAY DIFFRACTION98
1.6894-1.71710.28921630.26513120X-RAY DIFFRACTION97
1.7171-1.74670.2561630.25783115X-RAY DIFFRACTION97
1.7467-1.77840.27051640.22723114X-RAY DIFFRACTION98
1.7784-1.81260.27491650.22783121X-RAY DIFFRACTION97
1.8126-1.84960.25281670.22353144X-RAY DIFFRACTION98
1.8496-1.88990.27261650.2223172X-RAY DIFFRACTION97
1.8899-1.93380.22981640.21723101X-RAY DIFFRACTION97
1.9338-1.98220.22381700.21643166X-RAY DIFFRACTION99
1.9822-2.03580.2311650.20563176X-RAY DIFFRACTION98
2.0358-2.09570.2081630.19813132X-RAY DIFFRACTION97
2.0957-2.16330.23471670.19083170X-RAY DIFFRACTION98
2.1633-2.24060.24081680.19783194X-RAY DIFFRACTION98
2.2406-2.33040.21951680.19323192X-RAY DIFFRACTION98
2.3304-2.43640.22881680.1983182X-RAY DIFFRACTION99
2.4364-2.56490.22821690.20653214X-RAY DIFFRACTION99
2.5649-2.72550.21591720.19943245X-RAY DIFFRACTION99
2.7255-2.9360.21451690.20063211X-RAY DIFFRACTION99
2.936-3.23130.22741720.19343275X-RAY DIFFRACTION99
3.2313-3.69880.22541730.18073252X-RAY DIFFRACTION99
3.6988-4.65940.20291730.17783331X-RAY DIFFRACTION99
4.6594-47.57670.23431830.21133460X-RAY DIFFRACTION99

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