3JA5 | pdb_00003ja5

Genome and RdRp structure within the capsid of no-transcribing cypovirus

• PDB DOI: https://doi.org/10.2210/pdb3JA5/pdb
• EM Map EMD-6322: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Bombyx mori cypovirus 1
• Mutation(s): No 


• Deposited: 2015-04-21 Released: 2015-10-28 
• Deposition Author(s): Liu, H., Cheng, L.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 12.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM shows the polymerase structures and a nonspooled genome within a dsRNA virus.

Liu, H., Cheng, L.

(2015) Science 349: 1347-1350

• PubMed: 26383954 
• DOI: https://doi.org/10.1126/science.aaa4938
• Primary Citation Related Structures: 
  3JA4, 3JA5


• PubMed Abstract: 
  

  Double-stranded RNA (dsRNA) viruses possess a segmented dsRNA genome and a number of RNA-dependent RNA polymerases (RdRps) enclosed in a capsid. Until now, the precise structures of genomes and RdRps within the capsids have been unknown. Here we report the structures of RdRps and associated RNAs within nontranscribing and transcribing cypoviruses (NCPV and TCPV, respectively), using a combination of cryo-electron microscopy (cryo-EM) and a symmetry-mismatch reconstruction method. The RdRps and associated RNAs appear to exhibit a pseudo-D3 symmetric organization in both NCPV and TCPV. However, the molecular interactions between RdRps and the genomic RNA were found to differ in these states. Our work provides insight into the mechanisms of the replication and transcription in dsRNA viruses and paves a way for structural determination of lower-symmetry complexes enclosed in higher-symmetry structures.

---

Organizational Affiliation: 
• College of Physics and Information Science, Hunan Normal University, Changsha, Hunan 410081, China. [e-mail] [e-mail].
School of Life Sciences, Tsinghua University, Beijing 100084, China. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 138.83 kDa 
• Atom Count: 1,074 
• Modeled Residue Count: 1,074 
• Deposited Residue Count: 1,225 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-dependent RNA polymerase	A	1,225	Bombyx mori cypovirus 1	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for Q6RJR5 (Bombyx mori cytoplasmic polyhedrosis virus) Explore Q6RJR5  Go to UniProtKB:  Q6RJR5

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 12.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	MRC

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Liu, H., Cheng, L.

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2018-06-20
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.2: 2019-12-18
  Changes: Data collection
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references