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- PDB-5lts: Crystal structure of Lymphocytic choriomeningitis mammarenavirus ... -

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Basic information

Entry
Database: PDB / ID: 5lts
TitleCrystal structure of Lymphocytic choriomeningitis mammarenavirus endonuclease Mutant D118A
ComponentsRNA-directed RNA polymerase L
KeywordsTRANSFERASE / Endonuclease / LCMV Arenavirus
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / cap snatching / virion component / host cell / Hydrolases; Acting on ester bonds / host cell cytoplasm / hydrolase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity ...RNA-templated viral transcription / negative stranded viral RNA replication / cap snatching / virion component / host cell / Hydrolases; Acting on ester bonds / host cell cytoplasm / hydrolase activity / RNA-directed RNA polymerase / RNA-directed 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 / : / 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 / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesLymphocytic choriomeningitis mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsSaez-Ayala, M. / Yekwa, E.L. / Canard, B. / Alvarez, K. / Ferron, F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR11-BSV8-0019 France
CitationJournal: IUCrJ / Year: 2018
Title: Crystal structures ofLymphocytic choriomeningitis virusendonuclease domain complexed with diketo-acid ligands.
Authors: Saez-Ayala, M. / Yekwa, E.L. / Carcelli, M. / Canard, B. / Alvarez, K. / Ferron, F.
History
DepositionSep 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 17, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,5075
Polymers47,3562
Non-polymers1513
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-25 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.825, 159.221, 52.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein RNA-directed RNA polymerase L / Protein L


Mass: 23678.162 Da / Num. of mol.: 2 / Mutation: D118A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymphocytic choriomeningitis mammarenavirus
Gene: L, KUE_IGS310002 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A059U382, UniProt: P14240*PLUS, RNA-directed RNA polymerase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0,1M pH 6, Isopropanol 3,5%, MnCl2 1mM

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.51→53.57 Å / Num. all: 73597 / Num. obs: 31183 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 73.38 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06018 / Net I/σ(I): 14.17
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.09 / CC1/2: 0.649 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimless0.5.27data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JSB

3jsb


Resolution: 2.51→79.61 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.93 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.321 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.33 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.213
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1004 4.76 %RANDOM
Rwork0.207 ---
obs0.208 21098 98.9 %-
Displacement parametersBiso mean: 74.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.0963 Å20 Å20 Å2
2--1.4403 Å20 Å2
3----2.5366 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.51→79.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 0 9 113 3185
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093120HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.164208HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1139SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes93HARMONIC2
X-RAY DIFFRACTIONt_gen_planes439HARMONIC5
X-RAY DIFFRACTIONt_it3120HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion19.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion406SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3623SEMIHARMONIC4
LS refinement shellResolution: 2.51→2.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.236 136 4.9 %
Rwork0.216 2637 -
all0.217 2773 -
obs--99.28 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.54720.7948-1.64681.4232-0.76751.1505-0.07640.7811-0.2139-0.27290.07610.08620.0128-0.20590.0003-0.03050.0311-0.02470.0108-0.0592-0.161714.55739.8742.9283
21.59630.97350.27162.39831.12460.90050.0301-0.3418-0.42980.45240.004-0.01590.27010.0578-0.0341-0.03670.07390.0363-0.09560.079-0.049538.728316.63067.0486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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