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- EMDB-11830: Nudaurelia capensis omega virus capsid: virus-like particles expr... -

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Basic information

Entry
Database: EMDB / ID: EMD-11830
TitleNudaurelia capensis omega virus capsid: virus-like particles expressed in Nicotiana benthamiana
Map dataPostprocessed map from Relion
Sample
  • Virus: Nudaurelia capensis omega virus
    • Protein or peptide: p70
    • Protein or peptide: p70
Function / homologyPeptidase N2 / Peptidase family A21 / Viral coat protein subunit / p70
Function and homology information
Biological speciesNudaurelia capensis omega virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsCastells-Graells R / Ribeiro JRS / Domitrovic T / Hesketh EL / Scarff CA / Johnson JE / Ranson NA / Lawson DM / Lomonossoff GP
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 12, 2020-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateAug 25, 2021-
Current statusAug 25, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7anm
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7anm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11830.png

Downloads & links

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Map

FileDownload / File: emd_11830.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map from Relion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 600 pix.
= 639. Å		1.07 Å/pix.
x 600 pix.
= 639. Å		1.07 Å/pix.
x 600 pix.
= 639. 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: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.254742 - 0.35927644
Average (Standard dev.)-4.4038294e-05 (±0.021197114)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 639.00006 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z639.000639.000639.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.2550.359-0.000

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Supplemental data

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Mask #1

Fileemd_11830_msk_1.map
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

Fileemd_11830_half_map_1.map
AnnotationRefine3D half map 1 from Relion
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

Fileemd_11830_half_map_2.map
AnnotationRefine3D half map 2 from Relion
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: all
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)
Host systemOrganism: Nicotiana benthamiana (plant) / Recombinant cell: leaf tissue / Recombinant plasmid: pEAQ-HT
Molecular weightTheoretical: 16.76 MDa
Virus shellShell ID: 1 / Name: coat / Diameter: 420.0 Å / T number (triangulation number): 4

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Macromolecule #1: p70

MacromoleculeName: p70 / type: protein_or_peptide / ID: 1
Details: There is an autocatalytic cleavage between Asn570 and Phe571. Terminal oxygen has been added to Asn570. There is an autocatalytic cleavage between Asn570 and Phe571. Terminal oxygen has been added to Asn570.
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

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Macromolecule #2: p70

MacromoleculeName: p70 / type: protein_or_peptide / ID: 2
Details: There is an autocatalytic cleavage between Asn570 and Phe571. Terminal oxygen has been added to Asn570. There is an autocatalytic cleavage between Asn570 and Phe571. Terminal oxygen has been added to Asn570.
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

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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: 5
GridMaterial: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 2788 / Average exposure time: 1.5 sec. / Average electron dose: 79.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1ohf

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 21395
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1ohf

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 18.9 / Target criteria: Correlation coefficient
Output model

PDB-7anm:
Nudaurelia capensis omega virus capsid: virus-like particles expressed in Nicotiana benthamiana

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