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- EMDB-11911: Nudaurelia capensis omega virus procapsid: virus-like particles e... -

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Basic information

Entry
Database: EMDB / ID: EMD-11911
TitleNudaurelia capensis omega virus procapsid: virus-like particles expressed in Nicotiana benthamiana
Map dataDensity improved map from phenix.resolve_cryo_em at 6.63 Ang resolution
Sample
  • Virus: Nudaurelia capensis omega virus
    • Protein or peptide: p70
  • Protein or peptide: p70
KeywordsICOSAHEDRAL VIRUS / AUTO-CATALYTIC CLEAVAGE / VIRUS MATURATION / TRANSIENT EXPRESSION / VIRUS LIKE PARTICLE
Function / homologyPeptidase N2 / Peptidase family A21 / virion component / Viral coat protein subunit / p70
Function and homology information
Biological speciesNudaurelia capensis omega virus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.63 Å
AuthorsCastells-Graells R / Ribeiro JRS
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9794 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L014130/1 United Kingdom
John Innes FoundationNone United Kingdom
CitationJournal: Commun Biol / Year: 2021
Title: Plant-expressed virus-like particles reveal the intricate maturation process of a eukaryotic virus.
Authors: Roger Castells-Graells / Jonas R S Ribeiro / Tatiana Domitrovic / Emma L Hesketh / Charlotte A Scarff / John E Johnson / Neil A Ranson / David M Lawson / George P Lomonossoff /
Abstract: Many virus capsids undergo exquisitely choreographed maturation processes in their host cells to produce infectious virions, and these remain poorly understood. As a tool for studying virus ...Many virus capsids undergo exquisitely choreographed maturation processes in their host cells to produce infectious virions, and these remain poorly understood. As a tool for studying virus maturation, we transiently expressed the capsid protein of the insect virus Nudaurelia capensis omega virus (NωV) in Nicotiana benthamiana and were able to purify both immature procapsids and mature capsids from infiltrated leaves by varying the expression time. Cryo-EM analysis of the plant-produced procapsids and mature capsids to 6.6 Å and 2.7 Å resolution, respectively, reveals that in addition to large scale rigid body motions, internal regions of the subunits are extensively remodelled during maturation, creating the active site required for autocatalytic cleavage and infectivity. The mature particles are biologically active in terms of their ability to lyse membranes and have a structure that is essentially identical to authentic virus. The ability to faithfully recapitulate and visualize a complex maturation process in plants, including the autocatalytic cleavage of the capsid protein, has revealed a ~30 Å translation-rotation of the subunits during maturation as well as conformational rearrangements in the N and C-terminal helical regions of each subunit.
History
DepositionOct 29, 2020-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ata
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ata
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11911.png

Downloads & links

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Map

FileDownload / File: emd_11911.map.gz / Format: CCP4 / Size: 43.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity improved map from phenix.resolve_cryo_em at 6.63 Ang resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
2.13 Å/pix.
x 225 pix.
= 479.25 Å		2.13 Å/pix.
x 225 pix.
= 479.25 Å		2.13 Å/pix.
x 225 pix.
= 479.25 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.007
Minimum - Maximum-0.063345045 - 0.108826414
Average (Standard dev.)-0.000000000000108 (±0.009031488)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin383838
Dimensions225225225
Spacing225225225
CellA=B=C: 479.25003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.132.132.13
M x/y/z225225225
origin x/y/z0.0000.0000.000
length x/y/z479.250479.250479.250
α/β/γ90.00090.00090.000
start NX/NY/NZ383838
NX/NY/NZ225225225
MAP C/R/S321
start NC/NR/NS383838
NC/NR/NS225225225
D min/max/mean-0.0630.109-0.000

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Supplemental data

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Mask #1

Fileemd_11911_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Postprocessed map from Relion at 7.1 Ang resolution

Fileemd_11911_additional_1.map
AnnotationPostprocessed map from Relion at 7.1 Ang resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Refine3D half map 1 from Relion at 7.52 Ang resolution

Fileemd_11911_half_map_1.map
AnnotationRefine3D half map 1 from Relion at 7.52 Ang resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Refine3D half map 2 from Relion at 7.52 Ang resolution

Fileemd_11911_half_map_2.map
AnnotationRefine3D half map 2 from Relion at 7.52 Ang resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nudaurelia capensis omega virus

EntireName: Nudaurelia capensis omega virus
Components
  • Virus: Nudaurelia capensis omega virus
    • Protein or peptide: p70
  • Protein or peptide: p70

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Supramolecule #1: Nudaurelia capensis omega virus

SupramoleculeName: Nudaurelia capensis omega virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: The codon-optimized sequence was transiently expressed in Nicotiana benthamiana
NCBI-ID: 12541 / Sci species name: Nudaurelia capensis omega virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Gonimbrasia cytherea (butterflies/moths)
Molecular weightTheoretical: 16.76 MDa
Virus shellShell ID: 1 / Name: coat / Diameter: 480.0 Å / T number (triangulation number): 4

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Macromolecule #1: p70

MacromoleculeName: p70 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nudaurelia capensis omega virus
Molecular weightTheoretical: 62.094828 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MDSNSASGKR RSRNVRIAAN TVNVAPKQRQ ARGRRARSRA NNIDNVTAAA QELGQSLDAN VITFPTNVAT MPEFRSWARG KLDIDQDSI GWYFKYLDPA GATESARAVG EYSKIPDGLV KFSVDAEIRE IYNEECPTVS DASIPLDGAQ WSLSIISYPM F RTAYFAVA ...String:
MDSNSASGKR RSRNVRIAAN TVNVAPKQRQ ARGRRARSRA NNIDNVTAAA QELGQSLDAN VITFPTNVAT MPEFRSWARG KLDIDQDSI GWYFKYLDPA GATESARAVG EYSKIPDGLV KFSVDAEIRE IYNEECPTVS DASIPLDGAQ WSLSIISYPM F RTAYFAVA NVDNKEISLD VTNDLIVWLN NLASWRDVVD SGQWFTFSDD PTWFVRIRVL HPTYDLPDPT EGLLRTVSDY RL TYKSITC EANMPTLVDQ GFWIGGHYAL TPIATTQNAV EGSGFVHPFN VTRPGIAAGV TLTWASMPPG GSAPSGDPAW IPD STTQFQ WRHGGFDAPT GVITYTIPRG YTMQYFDTTT NEWNGFANPD DVVTFGQTGG AAGTNATITI TAPTVTLTIL ATTT SAANV INFRNLDAET TAASNRSEVP LPPLTFGQTA PNNPKIEQTL VKDTLGSYLV HSKMRNPVFQ LTPASSFGAI SFTNP GFDR NLDLPGFGGI RDSLDVNMST AVCHFRSLSK SCSIVTKTYQ GWEGVTNVNT PFGQFAHSGL LKNDEILCLA DDLATR LTG VYGATDN

UniProtKB: p70

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Macromolecule #2: p70

MacromoleculeName: p70 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Nudaurelia capensis omega virus
Molecular weightTheoretical: 7.815102 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString:
FAAAVLAFAA NMLTSVLKSE ATTSVIKELG NQATGLANQG LARLPGLLAS IPGKIAARVR ARRDRRRAAR MNNN

UniProtKB: p70

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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

Concentration0.3 mg/mL
BufferpH: 7.6
GridMaterial: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / 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 / Number grids imaged: 1 / Number real images: 8554 / Average exposure time: 1.5 sec. / Average electron dose: 72.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 75000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6anm

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 6.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 5426
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7anm


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe model was built and refined against a density modified map generated using phenix.resolve_cryo_em. This used the Relion half maps as inputs and improved the resolution to 6.6 Angstrom.
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 105.8 / Target criteria: Correlation coefficient
Output model

PDB-7ata:
Nudaurelia capensis omega virus procapsid: virus-like particles expressed in Nicotiana benthamiana

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