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- EMDB-12270: Cryo-EM structure of Pepper cryptic virus 1 VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-12270
TitleCryo-EM structure of Pepper cryptic virus 1 VLP
Map dataCryo-EM structure of PCV-1 VLP.
Sample
  • Virus: Pepper cryptic virus 1
    • Protein or peptide: Coat protein
KeywordsPartitivirus / Virus like particle / Capsid
Function / homologyviral capsid / membrane / Coat protein
Function and homology information
Biological speciesPepper cryptic virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsByrne MJ / Sainsbury F
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00160X/1 United Kingdom
CitationJournal: To Be Published
Title: Structure of Pepper Cryptic Virus 1 VLP
Authors: Byrne MJ / Sainsbury F / Ranson NA / Kashyap A / Esquirol L
History
DepositionJan 29, 2021-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ncr
  • Surface level: 0.034
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ncr
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12270.png

Downloads & links

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Map

FileDownload / File: emd_12270.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of PCV-1 VLP.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 545.28 Å		1.07 Å/pix.
x 512 pix.
= 545.28 Å		1.07 Å/pix.
x 512 pix.
= 545.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.034 / Movie #1: 0.034
Minimum - Maximum-0.09080416 - 0.18962151
Average (Standard dev.)-0.00083095836 (±0.010005922)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 545.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z545.280545.280545.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0910.190-0.001

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Supplemental data

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Sample components

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Entire : Pepper cryptic virus 1

EntireName: Pepper cryptic virus 1
Components
  • Virus: Pepper cryptic virus 1
    • Protein or peptide: Coat protein

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Supramolecule #1: Pepper cryptic virus 1

SupramoleculeName: Pepper cryptic virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 369643 / Sci species name: Pepper cryptic virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes

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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: Pepper cryptic virus 1
Molecular weightTheoretical: 47.626285 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MGDRVNAQDD DTVVPHQAPL QPAALQQDLT RSADYLLDNV RIGNHRQRYD KYRRYVLLRS SEIFTSLVAI YAHIFSSYWQ HFRRFTDQF QAPTGVQLPT FVARVYISTW LHDLYCSIRE ATRSISPLAF NERYSYELLP YSTEYDPFLA FLSMSIKPTH I QHTPENTL ...String:
MGDRVNAQDD DTVVPHQAPL QPAALQQDLT RSADYLLDNV RIGNHRQRYD KYRRYVLLRS SEIFTSLVAI YAHIFSSYWQ HFRRFTDQF QAPTGVQLPT FVARVYISTW LHDLYCSIRE ATRSISPLAF NERYSYELLP YSTEYDPFLA FLSMSIKPTH I QHTPENTL WIPILCENYD WDRNEANHNP FGITNFTLNS NLFYGLLAIL KERKEFKLST LTTNTIGRPC WLFDWHDNVQ VC AWFPREA NFNSQDVTAA YIIGVACTPK LGPSDDDAWK YYASLNSVPT FTPTEPRLTN RRSYGAYEVR TRETENNYFL PDS LLNIIE DFTATGTTQR RKIRRPSATS ASTGAAIIIR DTPGTASTAT TSTTETEVTF PPVIRTKIRD WYYHSRVILE LEDN SRTAA LRMFIIA

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

BufferpH: 7
Details: 20 mM MOPS, pH 7.0 with 140 mM NaCl and 5% (v/v) glycerol
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 1.12 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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