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- PDB-12ze: CryoEM structure of Papaya Meleira Virus (PMeV) particles purifie... -

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Basic information

Entry
Database: PDB / ID: 12ze
TitleCryoEM structure of Papaya Meleira Virus (PMeV) particles purified directly from Carica papaya latex
ComponentsCoat protein
KeywordsVIRUS / Papaya sticky disease / Double-stranded RNA viruses / Quasiequivalent conformation / Icosahedral capsid
Function / homologyviral capsid / Coat protein
Function and homology information
Biological speciesCarica papaya (papaya)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
Authorsde Oliveira, G. / Rodrigues, S.
Funding support Brazil, 6items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)465395/2014-7 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)408046/2021-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)408340/2024-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)303914/2024-6 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)404972/2021-7 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)301052/2025-5 Brazil
CitationJournal: To Be Published
Title: Structural adaptation of a dsRNA virus enables persistence in plant latex and expands host range
Authors: de Oliveira, G. / Montovaneli, G. / Arruda, H. / Rios, V. / Cunha, M. / Maurastoni, M. / Amorim, G. / Abreu, E. / Ribeiro, S. / Sanches, M. / Zingali, R. / Almeida, F. / Santos, A. / ...Authors: de Oliveira, G. / Montovaneli, G. / Arruda, H. / Rios, V. / Cunha, M. / Maurastoni, M. / Amorim, G. / Abreu, E. / Ribeiro, S. / Sanches, M. / Zingali, R. / Almeida, F. / Santos, A. / Fernandes, A. / Ventura, J. / Silva, J. / Fernandes, P. / Rodrigues, S.
History
DepositionApr 23, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coat protein
B: Coat protein


Theoretical massNumber of molelcules
Total (without water)198,9462
Polymers198,9462
Non-polymers00
Water00
1
A: Coat protein
B: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)11,936,730120
Polymers11,936,730120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Coat protein
B: Coat protein
x 5


  • icosahedral pentamer
  • 995 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)994,72810
Polymers994,72810
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein
B: Coat protein
x 6


  • icosahedral 23 hexamer
  • 1.19 MDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)1,193,67312
Polymers1,193,67312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Coat protein


Mass: 99472.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Carica papaya (papaya) / References: UniProt: A0A172JTY4
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Papaya meleira virus / Type: VIRUS
Details: Structure of PMeV particles purified directly from Carica papaya latex.
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Papaya meleira virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Carica papaya
Virus shellName: Coat protein / Diameter: 490 nm / Triangulation number (T number): 1
Buffer solutionpH: 9
Buffer componentConc.: 0.01 M / Name: Borate
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Monodisperse Papaya Meleira virus (PMeV) particles purified from Carica papaya latex
Specimen supportDetails: Grid preparation conditions were optimized for papaya meleira virus (PMeV) samples using counter-sided blotting for 5 s on freshly glow-discharged lacey carbon grids (Ted Pella, #01895-F). ...Details: Grid preparation conditions were optimized for papaya meleira virus (PMeV) samples using counter-sided blotting for 5 s on freshly glow-discharged lacey carbon grids (Ted Pella, #01895-F). Glow discharge was performed for 45 s using an EMS GloQube. Grids were plunge-frozen using an EM GP2 (Leica Microsystems). The blotting arm height and position were adjusted, and a contact sensor was used to ensure reproducible blotting conditions.
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K
Details: Grids were plunge-frozen using an EM GP2 (Leica Microsystems). The blotting arm height and position were adjusted, and a contact sensor was used to ensure reproducible blotting conditions.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 215000 X / Calibrated magnification: 215000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 300 nm / Calibrated defocus min: 300 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 20 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 25357
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv.4.5.3particle selection
2PHENIX1.20.1_4487model refinement
5cryoSPARCv.4.5.3CTF correction
10cryoSPARCv.4.5.3initial Euler assignment
11cryoSPARCv.4.5.3final Euler assignment
12cryoSPARCv.4.5.3classification
13cryoSPARCv.4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 53162
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53162 / Algorithm: FOURIER SPACE / Num. of class averages: 20 / Symmetry type: POINT
Atomic model buildingB value: 60 / Protocol: BACKBONE TRACE / Space: REAL / Target criteria: Cross-correlation
Atomic model buildingDetails: The annotated coat protein sequence (GenBank accession no. AMU19319.1) and the segmented density maps were used as input for automated model building with ModelAngelo and DeepTracer, which ...Details: The annotated coat protein sequence (GenBank accession no. AMU19319.1) and the segmented density maps were used as input for automated model building with ModelAngelo and DeepTracer, which yielded highly similar models.
Source name: Other / Type: in silico model
RefinementHighest resolution: 2.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212905
ELECTRON MICROSCOPYf_angle_d0.48917551
ELECTRON MICROSCOPYf_dihedral_angle_d3.6911703
ELECTRON MICROSCOPYf_chiral_restr0.0431879
ELECTRON MICROSCOPYf_plane_restr0.0052276

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