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- PDB-5mv0: Structure of an N-terminal domain of a reptarenavirus L protein -

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Basic information

Entry
Database: PDB / ID: 5mv0
TitleStructure of an N-terminal domain of a reptarenavirus L protein
ComponentsL protein
KeywordsVIRAL PROTEIN / Arenavirus / polymerase / endonuclease / cap-snatching
Function / homology
Function and homology information


cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding
Similarity search - Function
RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
PHOSPHATE ION / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCAS virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsRosenthal, M. / Gogrefe, N. / Reguera, J. / Vogel, D. / Rauschenberger, B. / Cusack, S. / Gunther, S. / Reindl, S.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationRE 3712/1-1 Germany
German Research FoundationGU 883/1-1 Germany
German Research FoundationGU 883/4-1 Germany
CitationJournal: PLoS Pathog. / Year: 2017
Title: Structural insights into reptarenavirus cap-snatching machinery.
Authors: Rosenthal, M. / Gogrefe, N. / Vogel, D. / Reguera, J. / Rauschenberger, B. / Cusack, S. / Gunther, S. / Reindl, S.
History
DepositionJan 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Mar 14, 2018Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: L protein
B: L protein
C: L protein
D: L protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2258
Polymers94,8454
Non-polymers3804
Water11,169620
1
A: L protein
C: L protein
hetero molecules

B: L protein
D: L protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2258
Polymers94,8454
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
2
B: L protein
D: L protein
hetero molecules

A: L protein
C: L protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2258
Polymers94,8454
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Unit cell
Length a, b, c (Å)56.970, 112.342, 153.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
L protein


Mass: 23711.160 Da / Num. of mol.: 4 / Fragment: N-terminus, UNP residues 1-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAS virus / Production host: Escherichia coli (E. coli) / References: UniProt: J7HBG8
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 200, 2.5% PEG 3000, and 100 mM MES, pH 5.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.931→90.73 Å / Num. obs: 74927 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 15.33
Reflection shellResolution: 1.931→2 Å / Redundancy: 2 % / Num. unique obs: 7396 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLM7.1.3data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→90.73 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.5
RfactorNum. reflection% reflection
Rfree0.215 3753 5.01 %
Rwork0.173 --
obs0.175 74918 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.93→90.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6424 0 20 620 7064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076713
X-RAY DIFFRACTIONf_angle_d0.8659124
X-RAY DIFFRACTIONf_dihedral_angle_d14.3684220
X-RAY DIFFRACTIONf_chiral_restr0.0531062
X-RAY DIFFRACTIONf_plane_restr0.0051156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.931-1.95550.26351300.20932594X-RAY DIFFRACTION100
1.9555-1.98120.29961230.2072611X-RAY DIFFRACTION100
1.9812-2.00840.24011550.19992586X-RAY DIFFRACTION100
2.0084-2.0370.26271190.19762651X-RAY DIFFRACTION100
2.037-2.06750.27261250.1892574X-RAY DIFFRACTION100
2.0675-2.09980.23861350.18692627X-RAY DIFFRACTION100
2.0998-2.13420.25511420.17452601X-RAY DIFFRACTION100
2.1342-2.1710.23481370.16662609X-RAY DIFFRACTION100
2.171-2.21050.19671420.16682590X-RAY DIFFRACTION100
2.2105-2.2530.22731440.1672611X-RAY DIFFRACTION100
2.253-2.2990.21951370.16872625X-RAY DIFFRACTION100
2.299-2.3490.23051350.16382602X-RAY DIFFRACTION100
2.349-2.40360.20911340.16492602X-RAY DIFFRACTION100
2.4036-2.46370.22021520.16722635X-RAY DIFFRACTION100
2.4637-2.53040.18971420.1662606X-RAY DIFFRACTION100
2.5304-2.60480.22951550.16362604X-RAY DIFFRACTION100
2.6048-2.68890.22161180.16382648X-RAY DIFFRACTION100
2.6889-2.7850.18731700.16022572X-RAY DIFFRACTION100
2.785-2.89650.19121450.17522648X-RAY DIFFRACTION100
2.8965-3.02840.22741300.16632656X-RAY DIFFRACTION100
3.0284-3.1880.2131560.17532624X-RAY DIFFRACTION100
3.188-3.38780.20191290.17332661X-RAY DIFFRACTION100
3.3878-3.64940.22471290.16792674X-RAY DIFFRACTION100
3.6494-4.01660.19931420.15622675X-RAY DIFFRACTION100
4.0166-4.59780.17581460.15022676X-RAY DIFFRACTION100
4.5978-5.79260.211360.17842749X-RAY DIFFRACTION100
5.7926-90.82820.22361450.21162854X-RAY DIFFRACTION100

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