[English] 日本語
Yorodumi
- PDB-9r7u: RNA-free helical (h8.5) virus-like particle composed of PVA (isol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r7u
TitleRNA-free helical (h8.5) virus-like particle composed of PVA (isolate B11) coat protein
ComponentsCapsid protein
KeywordsVIRUS LIKE PARTICLE / potato virus A / virus-like particle / potyvirus / coat protein / helical
Function / homology
Function and homology information


nuclear-inclusion-a endopeptidase / helper-component proteinase / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / helical viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / symbiont-mediated suppression of host innate immune response ...nuclear-inclusion-a endopeptidase / helper-component proteinase / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / helical viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / symbiont-mediated suppression of host innate immune response / viral translational frameshifting / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Peptidase family C4 / Potyvirus P1 protease / Potyviridae polyprotein ...Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Peptidase family C4 / Potyvirus P1 protease / Potyviridae polyprotein / Protein P3 of Potyviral polyprotein / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain profile. / Potyviridae P1 protease domain profile. / Potyvirus NIa protease (NIa-pro) domain / Potyvirus NIa protease (NIa-pro) domain profile. / Potyvirus coat protein / Potyvirus coat protein / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesPotato virus A
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsKoritnik, N. / Kezar, A. / Podobnik, M.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research Agency Slovenia
CitationJournal: Commun Biol / Year: 2026
Title: Species-specific structural adaptation of the potyviral coat protein in virions and virus-like particles
Authors: Koritnik, N. / Kezar, A. / Kavcic, L. / Znidaric, M.T. / Leonardi, A. / De, S. / Pollari, M. / Makinen, K. / Podobnik, M.
History
DepositionMay 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 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
Aa: Capsid protein
Ab: Capsid protein
Ac: Capsid protein
Ad: Capsid protein
Ae: Capsid protein
Af: Capsid protein
Ag: Capsid protein
Ah: Capsid protein
Ai: Capsid protein
Aj: Capsid protein
Ak: Capsid protein
Al: Capsid protein
Am: Capsid protein
An: Capsid protein
Ao: Capsid protein
Ap: Capsid protein
Aq: Capsid protein
Ar: Capsid protein
As: Capsid protein
At: Capsid protein
Au: Capsid protein
Av: Capsid protein
Aw: Capsid protein
Ax: Capsid protein


Theoretical massNumber of molelcules
Total (without water)730,30724
Polymers730,30724
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 ...
Capsid protein / CP / Coat protein


Mass: 30429.461 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Potato virus A / Strain: isolate B11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q85197
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Virus-like particle composed of PVA (isolate B11) coat protein
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Potato virus A / Strain: isolate B11
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

EM software
IDNameCategory
2EPUimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -42.45 ° / Axial rise/subunit: 4.74 Å / Axial symmetry: C1
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185072 / Symmetry type: HELICAL

+
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