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- PDB-9r9x: ssRNA-containing helical virus-like particle composed of PepMoV c... -

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Basic information

Entry
Database: PDB / ID: 9r9x
TitlessRNA-containing helical virus-like particle composed of PepMoV coat protein
Components
  • Capsid protein
  • RNA (5'-R(P*UP*UP*UP*UP*U)-3')
KeywordsVIRUS LIKE PARTICLE / pepper mottle virus / 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
RNA / Genome polyprotein
Similarity search - Component
Biological speciesPepper mottle virus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.64 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 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Aa: Capsid protein
Ab: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ac: Capsid protein
Ad: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ae: Capsid protein
Af: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ag: Capsid protein
Ah: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ai: Capsid protein
Aj: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ak: Capsid protein
Al: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Am: Capsid protein
An: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ao: Capsid protein
Ap: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Aq: Capsid protein
Ar: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
As: Capsid protein
At: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Au: Capsid protein
Av: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Aw: Capsid protein
Ax: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ay: Capsid protein
Az: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ba: Capsid protein
Bb: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bc: Capsid protein
Bd: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Be: Capsid protein
Bf: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bg: Capsid protein
Bh: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bi: Capsid protein
Bj: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bk: Capsid protein
Bl: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bm: Capsid protein
Bn: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bo: Capsid protein
Bp: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bq: Capsid protein
Br: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bs: Capsid protein
Bt: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bu: Capsid protein
Bv: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Bw: Capsid protein
Bx: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
By: Capsid protein
Bz: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ca: Capsid protein
Cb: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Cc: Capsid protein
Cd: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ce: Capsid protein
Cf: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Cg: Capsid protein
Ch: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ci: Capsid protein
Cj: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Ck: Capsid protein
Cl: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Cm: Capsid protein
Cn: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Co: Capsid protein
Cp: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Cq: Capsid protein
Cr: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Cs: Capsid protein
Ct: RNA (5'-R(P*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)1,163,69172
Polymers1,163,69172
Non-polymers00
Water00
1


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

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Components

#1: Protein ...
Capsid protein / CP / Coat protein


Mass: 30838.873 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pepper mottle virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01500
#2: RNA chain ...
RNA (5'-R(P*UP*UP*UP*UP*U)-3')


Mass: 1485.872 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pepper mottle virus / Production host: Escherichia coli BL21 (bacteria)
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Virus-like particle composed of PepMoV coat protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Pepper mottle virus
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

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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)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -40.99 ° / Axial rise/subunit: 3.93 Å / Axial symmetry: C1
3D reconstructionResolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36808 / Symmetry type: HELICAL

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