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- EMDB-76875: CryoEM structure of Papaya Meleira Virus (PMeV) particles purifie... -

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Basic information

Entry
Database: EMDB / ID: EMD-76875
TitleCryoEM structure of Papaya Meleira Virus (PMeV) particles purified directly from Carica papaya latex
Map dataPapaya Meleira Virus (PMeV) particles obtained directly from Carica papaya latex.
Sample
  • Virus: Papaya meleira virus
    • Protein or peptide: Coat protein
KeywordsPapaya sticky disease / Double-stranded RNA viruses / Quasiequivalent conformation / Icosahedral capsid / VIRUS
Function / homologyviral capsid / Coat protein
Function and homology information
Biological speciesCarica papaya (papaya) / Papaya meleira virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
Authorsde Oliveira G / Rodrigues S
Funding support Brazil, 6 items
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 / Fernandes A / Ventura J / Silva J ...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, 2026-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76875.png

Downloads & links

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Map

FileDownload / File: emd_76875.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPapaya Meleira Virus (PMeV) particles obtained directly from Carica papaya latex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 512 pix.
= 614.4 Å		1.2 Å/pix.
x 512 pix.
= 614.4 Å		1.2 Å/pix.
x 512 pix.
= 614.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-1.4795651 - 3.5520942
Average (Standard dev.)0.003803737 (±0.2111132)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 614.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Papaya Meleira Virus (PMeV) particles half map

Fileemd_76875_half_map_1.map
AnnotationPapaya Meleira Virus (PMeV) particles half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Papaya Meleira Virus (PMeV) particles half map

Fileemd_76875_half_map_2.map
AnnotationPapaya Meleira Virus (PMeV) particles half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Papaya meleira virus

EntireName: Papaya meleira virus
Components
  • Virus: Papaya meleira virus
    • Protein or peptide: Coat protein

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Supramolecule #1: Papaya meleira virus

SupramoleculeName: Papaya meleira virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Structure of PMeV particles purified directly from Carica papaya latex.
NCBI-ID: 1497848 / Sci species name: Papaya meleira virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Carica papaya (papaya)
Virus shellShell ID: 1 / Name: Coat protein / Diameter: 490.0 Å / T number (triangulation number): 1

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Carica papaya (papaya)
Molecular weightTheoretical: 99.47275 KDa
SequenceString: NENIIDSQRR NKAIPEYNTI LVPQVKELGN SQLIPSEYLL SNDYEGLEYS YDRYFGTIPQ SFIFSPADLK LDVDNKVITV NRQTELFTE FPREVCRLSE TSYTNQEYII MSSINQAKAN SYKVKRLASG LVTKDNIPIL PQYSSCMDVI KGRDISPSAR K TIDEAFQI ...String:
NENIIDSQRR NKAIPEYNTI LVPQVKELGN SQLIPSEYLL SNDYEGLEYS YDRYFGTIPQ SFIFSPADLK LDVDNKVITV NRQTELFTE FPREVCRLSE TSYTNQEYII MSSINQAKAN SYKVKRLASG LVTKDNIPIL PQYSSCMDVI KGRDISPSAR K TIDEAFQI HRCYGTNVSR SGSSYETLRR SRFNQVYDLY NNVSSGQSYV RLYYRLFTRW AQAQMAQVLN ERNTIYSPKE FK PQNLQWE YTSNNVAVRR DSVHYLASTG DGKYGNILKG NYNFGNNHIY DGEYSLFGHA TDMFRKIQNG SAFFLDAEGL SHD VIREIC CCAIDINEGN QPWLGITVGS DDTHVLKTKF TIPGLYYQCE GVSDIIIHWG ATEPEDVIPL RDLINVNFPD PGLR NSTGQ LSDNNLPWPE FTNFGLATAP INLSTIEEAI RIMVARTHSA EEARLAFELV MSRMLMIDVS KSPCYNGNQD SPTGS TLNE THYPLSTEWH RESNTSHIEK ANAHKSRFIQ PTGANELRLP YVFSGLAYFD FMFHEMTIPS PLWEATIMKG NQFINH SFI ITHALSVSIN WPSHTFSVDG GILDLAHNSP LTTPNMLNCP LAKRHINWLN KQSRQETPSI WSMCHKRATS VMYGFTL SD YFWLTGPRIP RDFYLTNSPI YLSHPYRLGW MIKKIPIHMV LPSASLQPLW PKQEWTPKVY SNEIQSRVRV GRSFPVFQ G FNWLQDGGMN FSLQYYLGIH NNNKYRYETP QWNDNTIQLA SWDVPMQTEF PTAPRFINPI FTGPCNSNDI LDNYMVPGF VRNYDFTTNR VKANGAKVFE ENTDAQKYLI HLVWQRIIDG KQLTVPSISV IPPSGMPIQD LYDNEY

UniProtKB: Coat protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 9 / Component - Concentration: 0.01 M / Component - Name: Borate
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. / Pretreatment - Atmosphere: AIR
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). ...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.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: LEICA EM GP
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..
DetailsMonodisperse Papaya Meleira virus (PMeV) particles purified from Carica papaya latex

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 25357 / Average exposure time: 5.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.3 µm / Calibrated magnification: 215000 / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 215000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 53162
CTF correctionSoftware - Name: cryoSPARC (ver. v.4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Details: Approximately 700 particles were manually picked and extracted to generate templates through two-dimensional (2D) classification. An initial ab initio three-dimensional reconstruction was ...Details: Approximately 700 particles were manually picked and extracted to generate templates through two-dimensional (2D) classification. An initial ab initio three-dimensional reconstruction was generated using a subset of 20000 particles with a maximum resolution of 6 Angstrons, an initial resolution of 35 Angstrons, C1 symmetry, 200 final iterations, and a class similarity parameter of 0.1. The resulting volume clearly revealed icosahedral symmetry.
Final reconstructionNumber classes used: 20 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v.4.5.3) / Number images used: 53162
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v.4.5.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v.4.5.3)
Final 3D classificationNumber classes: 30 / Avg.num./class: 2531 / Software - Name: cryoSPARC (ver. v.4.5.3)
Details: Two-dimensional classification was performed using 30 initial classes, a maximum alignment and classification resolution of 6 Angstrons, an initial classification uncertainty factor of 4, a ...Details: Two-dimensional classification was performed using 30 initial classes, a maximum alignment and classification resolution of 6 Angstrons, an initial classification uncertainty factor of 4, a circular mask diameter of 500 Angstrons, an outer circular mask diameter of 520 Angstrons, and 15 final full iterations, resulting in well-defined and homogeneous classes.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model
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 ...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.
RefinementSpace: REAL / Protocol: BACKBONE TRACE / Overall B value: 60 / Target criteria: Cross-correlation
Output model

PDB-12ze:
CryoEM structure of Papaya Meleira Virus (PMeV) particles purified directly from Carica papaya latex

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