9JJJ | pdb_00009jjj

Cryo-EM structure of a T=3 VLP of RHDV GI.2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Near-atomic structures of RHDV reveal insights into capsid assembly and different conformations between mature virion and VLP.

Ruan, Z.Shao, Q.Song, Y.Hu, B.Fan, Z.Wei, H.Liu, Y.Wang, F.Fang, Q.

(2024) J Virol 98: e0127524-e0127524

  • DOI: https://doi.org/10.1128/jvi.01275-24
  • Primary Citation of Related Structures:  
    9JJG, 9JJH, 9JJI, 9JJJ

  • PubMed Abstract: 

    Rabbit hemorrhagic disease virus (RHDV) poses a significant threat to rabbits, causing substantial economic losses in rabbit farming. The virus also endangers wild populations of rabbit species and the predatory animals that rely on rabbits as a food source, thereby disturbing the ecological balance. However, the structural understanding of RHDV has been limited due to the lack of high-resolution structures. Here, we present the first high-resolution cryo-EM structures of the mature virion and virus-like particles (VLPs) derived from both full-length and N-terminal arm (NTA)-truncated VP60. These structures reveal intricate structural details of the icosahedral capsid and crucial NTA-mediated interactions essential for capsid assembly. In addition, dramatic conformational differences are unexpectedly observed between the mature virion and VLP. The protruding spikes of the A-B dimers adopt a "raised" state in the mature virion and a "resting" state in the VLP. These findings enhance our understanding of the structure, assembly, and conformational dynamics of the RHDV capsid, laying the essential groundwork for further virological research and therapeutic advancements.IMPORTANCERHDV is a pathogen with significant economic and ecological impact. By presenting the first high-resolution cryo-EM structures of RHDV, we have uncovered detailed interactions among neighboring VP60 subunits of the icosahedral capsid. The NTA of VP60 is uniquely clustered around the threefold axis of the capsid, probably play a critical role in dragging the six VP60 dimers around the threefold axis during capsid assembly. Additionally, we observed dramatic conformational differences between the mature virion and VLPs. VLPs are commonly used for vaccine development, under the assumption that their structure closely resembles that of the mature virion. Our findings significantly advance the understanding of the RHDV capsid structure, which may be used for developing potential therapeutic strategies against RHDV.


  • Organizational Affiliation

    School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein
A, B, C
579Rabbit hemorrhagic disease virus 2Mutation(s): 0 
UniProt
Find proteins for A0A7M4BDB7 (Rabbit hemorrhagic disease virus 2)
Explore A0A7M4BDB7 
Go to UniProtKB:  A0A7M4BDB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7M4BDB7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0
MODEL REFINEMENTPHENIX1.19

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
100 Talents Plan Foundation of Sun Yat-sen UniversityChina--
China Agriculture Research SystemChinaCARS-43-C-1
Jiangsu Provincial Agricultural Science and TechnologyChinaCX(23)1028
Shenzhen Science and Technology ProgramChinaZDSYS20230626091203007

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-12-04
    Changes: Data collection, Database references
  • Version 1.3: 2025-01-22
    Changes: Data collection, Database references