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- EMDB-15209: Nudaurelia capensis omega virus maturation intermediate captured ... -

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Basic information

Entry
Database: EMDB / ID: EMD-15209
TitleNudaurelia capensis omega virus maturation intermediate captured at pH6.25 (insect cell expressed VLPs)
Map dataPostprocessed map from Relion
Sample
  • Virus: Nudaurelia capensis omega virus
    • Protein or peptide: p70
KeywordsICOSAHEDRAL VIRUS / AUTO-CATALYTIC CLEAVAGE / VIRUS MATURATION / VIRUS-LIKE PARTICLE / VIRUS LIKE PARTICLE
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: 4.8 Å
AuthorsCastells-Graells R / Hesketh EL / Johnson JE / Ranson NA / Lawson DM / Lomonossoff GP
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L014130/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9794 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
CitationJournal: To be published
Title: Decoding virus maturation with cryo-EM structures of intermediates
Authors: Castells-Graells R / Hesketh EL / Johnson JE / Ranson NA / Lawson DM / Lomonossoff GP
History
DepositionJun 17, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15209.png

Downloads & links

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Map

FileDownload / File: emd_15209.map.gz / Format: CCP4 / Size: 103 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.)
2.13 Å/pix.
x 300 pix.
= 639. Å		2.13 Å/pix.
x 300 pix.
= 639. Å		2.13 Å/pix.
x 300 pix.
= 639. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.046453275 - 0.12252846
Average (Standard dev.)0.0024965468 (±0.010038551)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 639.00006 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15209_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_15209_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_15209_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

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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: expressed in Spodoptera frugiperda Sf21 cells / 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: 460.0 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: 69.891953 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 VYGATDNFAA AVLAFAANML TSVLKSEATT SVIKELGNQA TGLANQGLAR LPGLLASIPG KIAARVRARR DRRRAAR MN NN

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: 6.25
GridMaterial: COPPER / Mesh: 400
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: 10528 / Average exposure time: 1.0 sec. / Average electron dose: 50.4 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: 2.2 µm / Nominal defocus min: 0.8 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:

8a3c

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.3) / Number images used: 114943
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.3)
Final 3D classificationSoftware - Name: RELION (ver. 3.0.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8a3c


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 432 / Target criteria: Correlation coefficient
Output model

PDB-8a6j:
Nudaurelia capensis omega virus maturation intermediate captured at pH6.25 (insect cell expressed VLPs)

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