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- PDB-6uct: Crystal structure of Mal de Rio Cuarto virus P9-1 viroplasm prote... -

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Entry
Database: PDB / ID: 6uct
TitleCrystal structure of Mal de Rio Cuarto virus P9-1 viroplasm protein (C-arm deletion mutant)
Componentsp9-1
KeywordsVIRAL PROTEIN / Fijivirus / MRCV / Wheat / Maize / Reoviridae / viroplasm
Function / homologyReovirus P9-like / Reovirus P9-like family / p9-1
Function and homology information
Biological speciesMal de Rio Cuarto virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 Å
AuthorsLlauger, G. / Klinke, S. / Monti, D. / Sycz, G. / Cerutti, M.L. / Goldbaum, F.A. / del Vas, M. / Otero, L.H.
Funding support Argentina, 4items
OrganizationGrant numberCountry
National Research Council (NRC, Argentina)PICT 2015-0621 Argentina
National Research Council (NRC, Argentina)PICT 2016-1425 Argentina
National Research Council (NRC, Argentina)PICT-2014-3754 Argentina
National Research Council (NRC, Argentina)PICT-2017-2537 Argentina
CitationJournal: mBio / Year: 2023
Title: A Fijivirus Major Viroplasm Protein Shows RNA-Stimulated ATPase Activity by Adopting Pentameric and Hexameric Assemblies of Dimers.
Authors: Gabriela Llauger / Roberto Melero / Demián Monti / Gabriela Sycz / Cristián Huck-Iriart / María L Cerutti / Sebastián Klinke / Evelyn Mikkelsen / Ariel Tijman / Rocío Arranz / Victoria ...Authors: Gabriela Llauger / Roberto Melero / Demián Monti / Gabriela Sycz / Cristián Huck-Iriart / María L Cerutti / Sebastián Klinke / Evelyn Mikkelsen / Ariel Tijman / Rocío Arranz / Victoria Alfonso / Sofía M Arellano / Fernando A Goldbaum / Yann G J Sterckx / José-María Carazo / Sergio B Kaufman / Pablo D Dans / Mariana Del Vas / Lisandro H Otero /
Abstract: Fijiviruses replicate and package their genomes within viroplasms in a process involving RNA-RNA and RNA-protein interactions. Here, we demonstrate that the 24 C-terminal residues (C-arm) of the P9-1 ...Fijiviruses replicate and package their genomes within viroplasms in a process involving RNA-RNA and RNA-protein interactions. Here, we demonstrate that the 24 C-terminal residues (C-arm) of the P9-1 major viroplasm protein of the mal de Río Cuarto virus (MRCV) are required for its multimerization and the formation of viroplasm-like structures. Using an integrative structural approach, the C-arm was found to be dispensable for P9-1 dimer assembly but essential for the formation of pentamers and hexamers of dimers (decamers and dodecamers), which favored RNA binding. Although both P9-1 and P9-1ΔC-arm catalyzed ATP with similar activities, an RNA-stimulated ATPase activity was only detected in the full-length protein, indicating a C-arm-mediated interaction between the ATP catalytic site and the allosteric RNA binding sites in the (do)decameric assemblies. A stronger preference to bind phosphate moieties in the decamer was predicted, suggesting that the allosteric modulation of ATPase activity by RNA is favored in this structural conformation. Our work reveals the structural versatility of a fijivirus major viroplasm protein and provides clues to its mechanism of action. The mal de Río Cuarto virus (MRCV) causes an important maize disease in Argentina. MRCV replicates in several species of plants and planthopper vectors. The viral factories, also called viroplasms, have been studied in detail in animal reovirids. This work reveals that a major viroplasm protein of MRCV forms previously unidentified structural arrangements and provides evidence that it may simultaneously adopt two distinct quaternary assemblies. Furthermore, our work uncovers an allosteric communication between the ATP and RNA binding sites that is favored in the multimeric arrangements. Our results contribute to the understanding of plant reovirids viroplasm structure and function and pave the way for the design of antiviral strategies for disease control.
History
DepositionSep 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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
Revision 1.2Feb 18, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: p9-1


Theoretical massNumber of molelcules
Total (without water)37,2571
Polymers37,2571
Non-polymers00
Water00
1
A: p9-1

A: p9-1


Theoretical massNumber of molelcules
Total (without water)74,5142
Polymers74,5142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)86.557, 86.557, 95.598
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein p9-1


Mass: 37256.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mal de Rio Cuarto virus / Plasmid: pET24a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: D9U542
Has protein modificationN

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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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 13% (w/v) PEG 8000, 0.2 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2019
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.47→47.8 Å / Num. obs: 5035 / % possible obs: 99.2 % / Redundancy: 24.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.027 / Rrim(I) all: 0.136 / Net I/σ(I): 15.8
Reflection shellResolution: 3.47→3.8 Å / Redundancy: 25.6 % / Rmerge(I) obs: 2.912 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1138 / CC1/2: 0.548 / Rpim(I) all: 0.582 / Rrim(I) all: 3.013 / % possible all: 96.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VJJ

3vjj


Resolution: 3.47→43.28 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.613
RfactorNum. reflection% reflectionSelection details
Rfree0.277 276 5.52 %RANDOM
Rwork0.22 ---
obs0.223 5004 99 %-
Displacement parametersBiso max: 281.62 Å2 / Biso mean: 185.21 Å2 / Biso min: 112.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.9738 Å20 Å20 Å2
2---0.9738 Å20 Å2
3---1.9476 Å2
Refinement stepCycle: final / Resolution: 3.47→43.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 0 0 2013
Num. residues----243
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d731SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes284HARMONIC5
X-RAY DIFFRACTIONt_it2049HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion269SEMIHARMONIC5
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_contact2354SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2049HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg2759HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.13
X-RAY DIFFRACTIONt_other_torsion22.71
LS refinement shellResolution: 3.47→3.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2735 89 6.64 %
Rwork0.2372 1252 -
all0.2395 1341 -
obs--96.54 %
Refinement TLS params.Method: refined / Origin x: 13.2924 Å / Origin y: -15.2388 Å / Origin z: -0.4668 Å
111213212223313233
T-0.0684 Å20.152 Å2-0.0123 Å2--0.0304 Å20.0741 Å2---0.1798 Å2
L7.9271 °2-2.9104 °2-1.3329 °2-5.7471 °20.5047 °2--5.7914 °2
S-0.1243 Å °-0.541 Å °-0.5442 Å °0.1089 Å °0.1491 Å °-0.3931 Å °0.5442 Å °0.5442 Å °-0.0249 Å °
Refinement TLS groupSelection details: { A|* }

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