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- PDB-5ls4: Mopeia virus exonuclease domain complexed with Calcium -

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Basic information

Entry
Database: PDB / ID: 5ls4
TitleMopeia virus exonuclease domain complexed with Calcium
ComponentsNucleoprotein
KeywordsHYDROLASE / Mopeia virus / exonuclease / Calcium / inhibitor
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 virus AN20410
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.469 Å
AuthorsYekwa, E.L. / Canard, B. / Ferron, F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-BSV8-0019 France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Activity inhibition and crystal polymorphism induced by active-site metal swapping.
Authors: Yekwa, E. / Khourieh, J. / Canard, B. / Papageorgiou, N. / Ferron, F.
History
DepositionAug 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Aug 23, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7754
Polymers23,5631
Non-polymers2123
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-10 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.962, 37.913, 48.986
Angle α, β, γ (deg.)90.00, 104.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1025-

HOH

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein


Mass: 23563.014 Da / Num. of mol.: 1 / Fragment: exonuclease domain, UNP residues 365-570
Source method: isolated from a genetically manipulated source
Details: Calcium / Source: (gene. exp.) Mopeia virus AN20410 / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S581
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#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.: 328 / 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: 2.56 Å3/Da / Density % sol: 52.1 %
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
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2015
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.469→47.52 Å / Num. obs: 40307 / % possible obs: 99.74 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.07341 / Net I/σ(I): 14.28
Reflection shellResolution: 1.469→1.521 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.4999 / Mean I/σ(I) obs: 2.8 / % possible all: 97.66

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LRP

5lrp


Resolution: 1.469→47.516 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.82
RfactorNum. reflection% reflection
Rfree0.197 3868 4.97 %
Rwork0.1702 --
obs0.1715 40307 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.469→47.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 9 328 1988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011701
X-RAY DIFFRACTIONf_angle_d1.2582283
X-RAY DIFFRACTIONf_dihedral_angle_d12.159662
X-RAY DIFFRACTIONf_chiral_restr0.073251
X-RAY DIFFRACTIONf_plane_restr0.006299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.469-1.48690.28641270.26282432X-RAY DIFFRACTION92
1.4869-1.50570.27761370.25282663X-RAY DIFFRACTION99
1.5057-1.52560.24821400.23912661X-RAY DIFFRACTION99
1.5256-1.54650.24531420.22792635X-RAY DIFFRACTION99
1.5465-1.56860.25721350.21792632X-RAY DIFFRACTION100
1.5686-1.5920.20621410.2132676X-RAY DIFFRACTION99
1.592-1.61680.23421360.20642611X-RAY DIFFRACTION99
1.6168-1.64340.24921410.19592704X-RAY DIFFRACTION99
1.6434-1.67170.26561400.20162671X-RAY DIFFRACTION100
1.6717-1.70210.23781360.1892592X-RAY DIFFRACTION99
1.7021-1.73480.21571410.18072667X-RAY DIFFRACTION99
1.7348-1.77020.19461400.17992666X-RAY DIFFRACTION100
1.7702-1.80870.23051390.17042694X-RAY DIFFRACTION100
1.8087-1.85080.19331360.16742605X-RAY DIFFRACTION100
1.8508-1.89710.18511440.16482689X-RAY DIFFRACTION100
1.8971-1.94840.1651370.16722628X-RAY DIFFRACTION100
1.9484-2.00570.17831380.15922659X-RAY DIFFRACTION99
2.0057-2.07050.17411370.15642644X-RAY DIFFRACTION99
2.0705-2.14450.1781430.16252655X-RAY DIFFRACTION100
2.1445-2.23030.1791370.15512653X-RAY DIFFRACTION99
2.2303-2.33180.19411310.15642621X-RAY DIFFRACTION99
2.3318-2.45480.17571340.16282658X-RAY DIFFRACTION100
2.4548-2.60850.21761390.1672609X-RAY DIFFRACTION99
2.6085-2.80990.22541410.17392683X-RAY DIFFRACTION99
2.8099-3.09270.20171360.1752672X-RAY DIFFRACTION100
3.0927-3.54010.1991340.16052638X-RAY DIFFRACTION100
3.5401-4.45960.18191430.14642641X-RAY DIFFRACTION99
4.4596-47.54060.14711430.15192661X-RAY DIFFRACTION100

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