[English] 日本語
Yorodumi
- EMDB-15209: Nudaurelia capensis omega virus maturation intermediate captured ... -

+
Open data


ID or keywords:

Loading...

-
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 / virion component / 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: Proc Natl Acad Sci U S A / Year: 2026
Title: Unraveling the maturation pathway of a eukaryotic virus through cryo-EM.
Authors: Roger Castells-Graells / Emma L Hesketh / Tsutomu Matsui / John E Johnson / Neil A Ranson / David M Lawson / George P Lomonossoff /
Abstract: Virus maturation is a fundamental biological process involving large-scale structural reorganizations that drive functional activation and lead to infectivity. Understanding the steps from the ...Virus maturation is a fundamental biological process involving large-scale structural reorganizations that drive functional activation and lead to infectivity. Understanding the steps from the initial procapsid assembly to mature virions is essential, both for comprehending viral life cycles and for developing antiviral therapies. However, capturing these steps has been challenging due to the transient and elusive nature of intermediate states. The nonenveloped, T = 4, ssRNA-containing, omega virus (NωV) is a highly accessible model system that exemplifies the maturation process of a eukaryotic virus. During maturation, the particle shrinks in outer diameter from 482 Å (pH 7.6) to 428 Å (pH 5.0). It is possible to mimic the maturation process in vitro by lowering the pH of a population of procapsids produced in heterologous systems. Indeed, by controlling the pH in vitro, it is possible to produce homogenous populations of intermediate NωV virus-like particles (VLPs) that occur too fleetingly to be observed in vivo. Here, we report structural models, based on cryoelectron microscopy (cryo-EM), of five intermediates in the NωV maturation process. The structures of the intermediate particles reveal unique, quaternary position-dependent trajectories and refolding of subunit N and C-terminal regions, including the formation of the autocatalytic cleavage site at N570. The detailed structures reported here, coupled with previously determined structures of the procapsids and mature particles, allow the maturation pathway to be described in detail for a eukaryotic virus.
History
DepositionJun 17, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15209.png

Downloads & links

-
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 °

-
Supplemental data

-
Mask #1

Fileemd_15209_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
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)

-
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)

-
Sample components

-
Entire : Nudaurelia capensis omega virus

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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 6.25
GridMaterial: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
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

+
Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
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)

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more