8A3C | pdb_00008a3c

Nudaurelia capensis omega virus maturation intermediate captured at pH5.9 (insect cell expressed VLPs)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Unraveling the maturation pathway of a eukaryotic virus through cryo-EM.

Castells-Graells, R.Hesketh, E.L.Matsui, T.Johnson, J.E.Ranson, N.A.Lawson, D.M.Lomonossoff, G.P.

(2026) Proc Natl Acad Sci U S A 123: e2420493123-e2420493123

  • DOI: https://doi.org/10.1073/pnas.2420493123
  • Primary Citation of Related Structures:  
    8A3C, 8A41, 8A6J, 8AAY, 8AC6, 8ACH

  • PubMed 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 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, Nudaurelia capensis 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.


  • Organizational Affiliation
    • Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
p70
A, B, C, D
644Nudaurelia capensis omega virusMutation(s): 0 
UniProt
Find proteins for Q4TVS9 (Nudaurelia capensis omega virus)
Explore Q4TVS9 
Go to UniProtKB:  Q4TVS9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4TVS9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.3
MODEL REFINEMENTPHENIX1.20rc4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/L014130/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBBS/E/J/000PR9794
Wellcome TrustUnited Kingdom108466/Z/15/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Data collection, Refinement description
  • Version 1.2: 2026-03-18
    Changes: Data collection, Database references, Structure summary