[English] 日本語
Yorodumi
- PDB-9qy3: Structure of the Plum Pox Virus (PPV) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qy3
TitleStructure of the Plum Pox Virus (PPV)
Components
  • Coat Protein (CP)
  • RNA
KeywordsVIRUS / Potyvirus / Plum Pox Virus / PPV
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / RNA / RNA (> 10) / RNA (> 100) / Genome polyprotein
Function and homology information
Biological speciesPlum pox virus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBonnet, D.M.V. / Chaves-Sanjuan, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca Italy
CitationJournal: Arch Virol / Year: 2025
Title: Structural characterization of plum pox virus by cryo-electron microscopy.
Authors: Diane Marie Valérie Jeanne Bonnet / Antonio Chaves-Sanjuan / Nicoletta Contaldo / Angelo De Stradis / Rosanna Caliandro / Angelantonio Minafra / Filippo Geuna /
Abstract: Plum pox virus (PPV), a significant member of the genus Potyvirus, represents a global agricultural challenge, causing significant economic losses and threatening fruit farming due to its easy ...Plum pox virus (PPV), a significant member of the genus Potyvirus, represents a global agricultural challenge, causing significant economic losses and threatening fruit farming due to its easy transmission to most Prunus species. Here, we present the high-resolution structural characterization of PPV using cryo-electron microscopy (cryo-EM). The reconstructed structure at 2.9 Å reveals a filamentous virion with a helical assembly formed by the coat protein (CP), which encapsidates a single-stranded RNA (ssRNA) genome. The structure of the CP core shows remarkable conservation with other potyviruses, with an RNA binding site and inter-subunit interactions mediated in part by the N-terminal arm, which is confirmed here to have a disordered structure. Mass spectrometry analysis identified numerous post-translational modifications, mostly phosphorylation, primarily in the flexible N-terminal region. In silico predictions revealed intrinsically disordered regions, which is compatible with the amyloidogenic properties of the CP. These results provide new insights into the architecture and assembly of PPV, offering a basis for future studies and, possibly, antiviral strategies.
History
DepositionApr 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Coat Protein (CP)
B: Coat Protein (CP)
C: Coat Protein (CP)
D: Coat Protein (CP)
E: Coat Protein (CP)
F: Coat Protein (CP)
G: Coat Protein (CP)
H: Coat Protein (CP)
I: Coat Protein (CP)
J: Coat Protein (CP)
K: Coat Protein (CP)
L: Coat Protein (CP)
M: Coat Protein (CP)
N: Coat Protein (CP)
O: Coat Protein (CP)
P: Coat Protein (CP)
Q: Coat Protein (CP)
R: Coat Protein (CP)
S: Coat Protein (CP)
T: Coat Protein (CP)
U: Coat Protein (CP)
V: Coat Protein (CP)
W: Coat Protein (CP)
X: Coat Protein (CP)
Y: Coat Protein (CP)
Z: Coat Protein (CP)
a: Coat Protein (CP)
b: Coat Protein (CP)
c: Coat Protein (CP)
d: Coat Protein (CP)
e: Coat Protein (CP)
f: Coat Protein (CP)
g: Coat Protein (CP)
h: Coat Protein (CP)
i: Coat Protein (CP)
j: Coat Protein (CP)
k: Coat Protein (CP)
l: Coat Protein (CP)
m: Coat Protein (CP)
n: Coat Protein (CP)
o: Coat Protein (CP)
p: Coat Protein (CP)
q: Coat Protein (CP)
r: Coat Protein (CP)
s: Coat Protein (CP)
t: RNA


Theoretical massNumber of molelcules
Total (without water)1,835,84346
Polymers1,835,84346
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein ...
Coat Protein (CP)


Mass: 36551.996 Da / Num. of mol.: 45
Source method: isolated from a genetically manipulated source
Details: Coat Protein (CP) / Source: (gene. exp.) Plum pox virus / Production host: Plum pox virus / References: UniProt: B6C7W4
#2: RNA chain RNA


Mass: 191003.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plum pox virus / Production host: Plum pox virus
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: Plum pox virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Plum pox virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Virus shellName: CP
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2508

-
Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPU2.8image acquisition
4CTFFIND4CTF correction
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIX1.19.2_4158model refinement
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: -40.89 ° / Axial rise/subunit: 4.08 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 406769
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 406769 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementHighest resolution: 2.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00680054
ELECTRON MICROSCOPYf_angle_d0.618109481
ELECTRON MICROSCOPYf_dihedral_angle_d8.26112912
ELECTRON MICROSCOPYf_chiral_restr0.04611880
ELECTRON MICROSCOPYf_plane_restr0.00613770

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more