7CZ6 | pdb_00007cz6

Protrusion structure of Omono River virus

• PDB DOI: https://doi.org/10.2210/pdb7CZ6/pdb
• EM Map EMD-30507: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Omono River virus
• Mutation(s): No 


• Deposited: 2020-09-07 Released: 2021-03-03 
• Deposition Author(s): Shao, Q., Jia, X., Gao, Y., Liu, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM reveals a previously unrecognized structural protein of a dsRNA virus implicated in its extracellular transmission.

Shao, Q., Jia, X., Gao, Y., Liu, Z., Zhang, H., Tan, Q., Zhang, X., Zhou, H., Li, Y., Zhang, Q.

(2021) PLoS Pathog 17: e1009396-e1009396

• PubMed: 33730056 
• DOI: https://doi.org/10.1371/journal.ppat.1009396
• Primary Citation Related Structures: 
  7CZ6, 7D0K, 7D0L


• PubMed Abstract: 
  

  Mosquito viruses cause unpredictable outbreaks of disease. Recently, several unassigned viruses isolated from mosquitoes, including the Omono River virus (OmRV), were identified as totivirus-like viruses, with features similar to those of the Totiviridae family. Most reported members of this family infect fungi or protozoans and lack an extracellular life cycle stage. Here, we identified a new strain of OmRV and determined high-resolution structures for this virus using single-particle cryo-electron microscopy. The structures feature an unexpected protrusion at the five-fold vertex of the capsid. Disassociation of the protrusion could result in several conformational changes in the major capsid. All these structures, together with some biological results, suggest the protrusions' associations with the extracellular transmission of OmRV.

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Organizational Affiliation: 
• State Key Lab for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
Guangdong Provincial Center for Disease Control and Prevention, Guangdong Provincial Institute of Public Health, Guangzhou, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 12.92 kDa 
• Atom Count: 907 
• Modeled Residue Count: 126 
• Deposited Residue Count: 126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A [auth C]	126	Omono River virus	Mutation(s): 0
UniProt
Find proteins for A0ACD6BAF6 (Omono River virus) Explore A0ACD6BAF6  Go to UniProtKB:  A0ACD6BAF6

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.17
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Shao, Q., Jia, X., Gao, Y., Liu, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31570736

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references, Derived calculations