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

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Basic information

Entry
Database: PDB / ID: 5ltn
TitleCrystal structure of Lymphocytic choriomeningitis mammarenavirus endonuclease complexed with DPBA
ComponentsRNA-directed RNA polymerase L
KeywordsTRANSFERASE / Endonuclease / LCMV Arenavirus DPBA
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
DI(HYDROXYETHYL)ETHER / 2-4-DIOXO-4-PHENYLBUTANOIC ACID / RNA-directed RNA polymerase L / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesLymphocytic choriomeningitis mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 of Lymphocytic 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 1.3Oct 16, 2019Group: Data collection / Database references / Category: citation / reflns / reflns_shell
Item: _citation.journal_abbrev / _citation.title ..._citation.journal_abbrev / _citation.title / _reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rrim_I_all / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all
Revision 1.4Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
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_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.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.value / _struct_conn.pdbx_dist_value / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,43117
Polymers47,4442
Non-polymers98715
Water4,125229
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-60 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.185, 107.185, 53.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 23722.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymphocytic choriomeningitis mammarenavirus
Gene: L, KUE_IGS320002 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A059U381, UniProt: P14240*PLUS, RNA-directed RNA polymerase

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Non-polymers , 7 types, 244 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-XI7 / 2-4-DIOXO-4-PHENYLBUTANOIC ACID


Mass: 192.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8O4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.26 Å3/Da / Density % sol: 62.24 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0,1M pH 6,2, Isopropanol 3,5%, MgCl2 1mM, DPBA 2mM

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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: 1.88→53.593 Å / Num. obs: 241187 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 37.53 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.105 / Net I/σ(I): 8.54
Reflection shellResolution: 1.88→1.947 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 1.05 / CC1/2: 0.416 / Rrim(I) all: 1.15 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimless0.5.12data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LTF

5ltf


Resolution: 1.88→53.593 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.6 / Phase error: 23.16
RfactorNum. reflection% reflection
Rfree0.2156 2457 4.93 %
Rwork0.1903 --
obs0.1915 49844 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.88→53.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3042 0 60 229 3331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013160
X-RAY DIFFRACTIONf_angle_d1.1014258
X-RAY DIFFRACTIONf_dihedral_angle_d18.9321950
X-RAY DIFFRACTIONf_chiral_restr0.061478
X-RAY DIFFRACTIONf_plane_restr0.006553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.91620.32891180.30552653X-RAY DIFFRACTION100
1.9162-1.95530.28211360.27622565X-RAY DIFFRACTION100
1.9553-1.99780.3031420.26062646X-RAY DIFFRACTION99
1.9978-2.04430.27441410.23862539X-RAY DIFFRACTION99
2.0443-2.09540.30081270.23832614X-RAY DIFFRACTION100
2.0954-2.15210.27561430.2282632X-RAY DIFFRACTION100
2.1521-2.21540.23261450.20932595X-RAY DIFFRACTION100
2.2154-2.28690.23711340.22192613X-RAY DIFFRACTION100
2.2869-2.36870.28341560.20922617X-RAY DIFFRACTION100
2.3687-2.46350.21971230.19682617X-RAY DIFFRACTION100
2.4635-2.57560.22061640.18982619X-RAY DIFFRACTION100
2.5756-2.71140.20151200.19772647X-RAY DIFFRACTION100
2.7114-2.88130.25811740.19832596X-RAY DIFFRACTION100
2.8813-3.10370.24681220.19272663X-RAY DIFFRACTION100
3.1037-3.4160.18731240.18142670X-RAY DIFFRACTION100
3.416-3.91020.20481110.17422687X-RAY DIFFRACTION100
3.9102-4.92590.16011420.1572671X-RAY DIFFRACTION100
4.9259-53.61430.20511350.18842743X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -55.7601 Å / Origin y: -15.3583 Å / Origin z: 2.1425 Å
111213212223313233
T0.2932 Å2-0.009 Å20.0497 Å2-0.2703 Å2-0.0014 Å2--0.2851 Å2
L0.406 °20.0305 °2-0.3325 °2--0.0054 °2-0.0794 °2--0.2566 °2
S-0.053 Å °-0.0052 Å °-0.0841 Å °-0.0456 Å °0.0211 Å °-0.0277 Å °0.0456 Å °0.014 Å °0.0029 Å °
Refinement TLS groupSelection details: all

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