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- PDB-5izh: Lassa virus L protein cap-snatching endonuclease. apo form -

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Basic information

Entry
Database: PDB / ID: 5izh
TitleLassa virus L protein cap-snatching endonuclease. apo form
ComponentsRNA-directed RNA polymerase L
KeywordsTRANSFERASE / cap-snatching nuclease Lassa transcription
Function / homology
Function and homology information


negative stranded viral RNA replication / cap snatching / virion component / host cell cytoplasm / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding
Similarity search - Function
Arenavirus RNA polymerase / RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / : / Glycosyl hydrolases family 10 (GH10) active site. / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Alpha-Beta Plaits ...Arenavirus RNA polymerase / RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / : / Glycosyl hydrolases family 10 (GH10) active site. / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesLassa mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsReguera, J. / Cusack, S.
Funding support France, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-ADG France
CitationJournal: Plos Pathog. / Year: 2016
Title: Comparative Structural and Functional Analysis of Bunyavirus and Arenavirus Cap-Snatching Endonucleases.
Authors: Reguera, J. / Gerlach, P. / Rosenthal, M. / Gaudon, S. / Coscia, F. / Gunther, S. / Cusack, S.
History
DepositionMar 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: RNA-directed RNA polymerase L


Theoretical massNumber of molelcules
Total (without water)39,3312
Polymers39,3312
Non-polymers00
Water3,567198
1
A: RNA-directed RNA polymerase L


Theoretical massNumber of molelcules
Total (without water)19,6661
Polymers19,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-directed RNA polymerase L


Theoretical massNumber of molelcules
Total (without water)19,6661
Polymers19,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.750, 60.130, 132.780
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 RNA-directed RNA polymerase L / Protein L


Mass: 19665.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa mammarenavirus / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q6GWS6, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: citrate 0.191 M PEG 3350 4% 0.1 M Hepes pH7 0.1 M strontium chloride 2mM MnCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.85→66.4 Å / Num. obs: 40510 / % possible obs: 99.5 % / Redundancy: 4.78 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 15.11
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.726

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JSB

3jsb


Resolution: 1.85→66.39 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 11.168 / SU ML: 0.139 / Cross valid method: FREE R-VALUE / ESU R: 0.19 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25931 2017 5 %RANDOM
Rwork0.20531 ---
obs0.20816 38459 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.225 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2--5.64 Å2-0 Å2
3----5.23 Å2
Refinement stepCycle: 1 / Resolution: 1.85→66.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 0 198 2932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192762
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9933732
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2855340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10525.161124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66915522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5941514
X-RAY DIFFRACTIONr_chiral_restr0.0920.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212024
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2324.0211366
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.8846.0081704
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3784.4151396
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.61638.34811765
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.89932762
X-RAY DIFFRACTIONr_sphericity_free39.956544
X-RAY DIFFRACTIONr_sphericity_bonded19.74352872
LS refinement shellResolution: 1.854→1.902 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 132 -
Rwork0.329 2769 -
obs--98.07 %

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