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- PDB-6t2a: Mopeia Virus Exonuclease domain partially complexed with Manganese -

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Basic information

Entry
Database: PDB / ID: 6t2a
TitleMopeia Virus Exonuclease domain partially complexed with Manganese
ComponentsNucleoprotein
KeywordsMETAL BINDING PROTEIN / 3-5 Exonuclease / complex
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / virus-mediated perturbation of host defense response ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / virus-mediated perturbation of host defense response / RNA binding / metal ion binding
Similarity search - Function
Nucleocapsid protein, arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, C-terminal superfamily / Arenavirus nucleocapsid N-terminal domain / Arenavirus nucleocapsid C-terminal domain
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Nucleoprotein
Similarity search - Component
Biological speciesMopeia mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsNguyen, T.H.V. / Ferron, F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-18-ASTR-0010-01 France
CitationJournal: Iucrj / Year: 2022
Title: Inhibition of Arenaviridae nucleoprotein exonuclease by bisphosphonate
Authors: Nguyen, T.H.V. / Yekwa, E. / Selisko, B. / Canard, B. / Alvarez, K. / Ferron, F.
History
DepositionOct 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4737
Polymers47,1262
Non-polymers3475
Water2,162120
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7894
Polymers23,5631
Non-polymers2263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6833
Polymers23,5631
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.597, 37.969, 137.379
Angle α, β, γ (deg.)90.000, 93.310, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 23563.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mopeia mammarenavirus / Gene: NP, N / Production host: Escherichia coli (E. coli)
References: UniProt: Q5S581, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M MES pH 6.5 and 25 % (M/W) PEG 8000)

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2018
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.758→137.151 Å / Num. obs: 44701 / % possible obs: 94.3 % / Redundancy: 3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.019 / Net I/σ(I): 17.1
Reflection shellResolution: 1.758→1.788 Å / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2273 / CC1/2: 0.965 / Rpim(I) all: 0.238

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDS20190315data reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SX8

6sx8


Resolution: 2→43.969 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0.82 / Phase error: 28.65
RfactorNum. reflection% reflection
Rfree0.2668 1981 6.61 %
Rwork0.2323 --
obs0.2345 29971 92.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.53 Å2 / Biso mean: 26.0674 Å2 / Biso min: 5.48 Å2
Refinement stepCycle: final / Resolution: 2→43.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 21 120 3292
Biso mean--50.79 39.87 -
Num. residues----395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.050.37631420.3725206598
2.05-2.10540.3616500.315373534
2.1054-2.16740.34251520.309208199
2.1674-2.23740.30881560.2777208097
2.2374-2.31730.31121400.2603198694
2.3173-2.41010.29271560.2442215299
2.4101-2.51980.31581540.2592210999
2.5198-2.65260.30641430.2567210899
2.6526-2.81880.33831500.2547212498
2.8188-3.03640.29661520.2558204196
3.0364-3.34180.221530.2287211598
3.3418-3.82510.24941450.2025215798
3.8251-4.81830.18961430.1691205995
4.8183-43.9690.20391450.1805217895
Refinement TLS params.Method: refined / Origin x: 8.0478 Å / Origin y: 29.7536 Å / Origin z: 34.3086 Å
111213212223313233
T0.1244 Å2-0.0974 Å2-0.0031 Å2-0.1027 Å20.0012 Å2--0.0804 Å2
L0.0009 °2-0.017 °20.0148 °2-0.1535 °2-0.0689 °2--0.044 °2
S-0.0054 Å °0.0171 Å °0.0027 Å °-0.1912 Å °-0.0053 Å °0.0311 Å °0.0915 Å °-0.0389 Å °-0.0613 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA365 - 570
2X-RAY DIFFRACTION1allA1 - 2
3X-RAY DIFFRACTION1allB366 - 1
4X-RAY DIFFRACTION1allB2
5X-RAY DIFFRACTION1allS2 - 132
6X-RAY DIFFRACTION1allC1

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