12ze

CryoEM structure of Papaya Meleira Virus (PMeV) particles purified directly from Carica papaya latex

Method: ELECTRON MICROSCOPY Dmax: 154.7 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Coat protein

OrganismNot specified

UniProt A0A172JTY4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 120 PDB declaration: 120-meric(120) Consistent with protein copy count Chain A; UniProt 274–1139 Chain B; UniProt 274–1139 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 9 cryo-EM vitrification conditions:Cryogen ETHANE;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. Resolution 2.60 Å
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 274–1139 Chain B; UniProt 274–1139 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 9 cryo-EM vitrification conditions:Cryogen ETHANE;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. Resolution 2.60 Å
3 Protein homooligomer Homooligomer Protein × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain A; UniProt 274–1139 Chain B; UniProt 274–1139 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 9 cryo-EM vitrification conditions:Cryogen ETHANE;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. Resolution 2.60 Å
4 Protein homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain A; UniProt 274–1139 Chain B; UniProt 274–1139 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 9 cryo-EM vitrification conditions:Cryogen ETHANE;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. Resolution 2.60 Å
5 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 274–1139 Chain B; UniProt 274–1139 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 9 cryo-EM vitrification conditions:Cryogen ETHANE;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. Resolution 2.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A172JTY4_9VIRU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–866; UniProt 274–1139 Author chain B; PDBConstruct 1–866; UniProt 274–1139

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 12ze

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 12ze
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2. Structure Basics 2. Structure Basics

Entry ID entry_id12ze
Deposition date deposition_date2026-04-23
Structure title titleCryoEM structure of Papaya Meleira Virus (PMeV) particles purified directly from Carica papaya latex
Keywords keywordsPapaya sticky disease, Double-stranded RNA viruses, Quasiequivalent conformation, Icosahedral capsid, VIRUS; VIRUS
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier44.89
Radius of gyration Rg (electron density) rg_electron44.81
Forward intensity I(0) i0463277000.00
Molecular weight molecular_weight177910.0 kDa
Excluded volume excluded_volume222840 ų
Envelope volume envelope_volume316700 ų
Hydration-shell volume shell_volume60732 ų
Envelope diameter envelope_diameter162.7
Shell Rg shell_rg47.11
Envelope Rg envelope_rg44.70
Shape Rg shape_rg44.83
Total Rg total_rg44.87
Total atoms total_atoms12559
Residues n_residues1551
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax154.7
Rg (real space) rg_real45.12
Rg uncertainty (real space) rg_real_error1.59
I(0) (real space) i0_real4.6330e+08
I(0) uncertainty (real space) i0_real_error7.7230e+06
Rg (reciprocal space) rg_reciprocal44.89
I(0) (reciprocal space) i0_reciprocal463200000.0000
Solution quality estimate total_estimate0.8528
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.2
Skewness Skewness skewness0.422
Kurtosis Kurtosis kurtosis-0.445
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha112000000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.842; Smooth: 0.773

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

8. Citations (1)

9. Files and Curves (10)