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- PDB-6sy8: Mopeia Virus Exonuclease domain fully depleted of Manganese un AL... -

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Basic information

Entry
Database: PDB / ID: 6sy8
TitleMopeia Virus Exonuclease domain fully depleted of Manganese un ALD compound
ComponentsNucleoprotein
KeywordsMETAL BINDING PROTEIN / 3-5 Exonuclease
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 / viral nucleocapsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / 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
Biological speciesMopeia virus AN20410
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsNguyen, T.H.V. / Ferron, F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency 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
DepositionSep 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 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)47,2574
Polymers47,1262
Non-polymers1312
Water2,108117
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6282
Polymers23,5631
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6282
Polymers23,5631
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.853, 38.290, 137.315
Angle α, β, γ (deg.)90.000, 92.630, 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 virus AN20410 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES 25 % (M/W) PEG 8000) 3mM Mn

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2018
Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.08→137.17 Å / Num. obs: 28863 / % possible obs: 99.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 37.23 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.058 / Rrim(I) all: 0.135 / Net I/σ(I): 10.6 / Num. measured all: 151996 / Scaling rejects: 2387
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.08-2.25.40.9932255241530.9420.4551.0962.499.4
6.59-137.174.40.05343279740.9960.0270.05925.399

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimless0.7.2data scaling
PDB_EXTRACT3.25data extraction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SX8

6sx8


Resolution: 2.08→68.58 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.856 / SU R Cruickshank DPI: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.235 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.199
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1346 4.66 %RANDOM
Rwork0.248 ---
obs0.25 28859 99.5 %-
Displacement parametersBiso max: 128.17 Å2 / Biso mean: 53.84 Å2 / Biso min: 20.87 Å2
Baniso -1Baniso -2Baniso -3
1--33.0693 Å20 Å210.9709 Å2
2--7.4012 Å20 Å2
3---25.6681 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: final / Resolution: 2.08→68.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 0 2 117 3302
Biso mean--40.18 50.75 -
Num. residues----397
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1160SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes550HARMONIC5
X-RAY DIFFRACTIONt_it3249HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion431SEMIHARMONIC5
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_contact3665SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3249HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4402HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion17.11
LS refinement shellResolution: 2.08→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2789 24 4.15 %
Rwork0.2727 554 -
all0.273 578 -
obs--97.76 %

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