Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A10B1C1 Local Symmetry: Cyclic - C5  (3D View)
Local Stoichiometry: Homo 10-mer - A10 

Local Symmetry: Cyclic - C5  (3D View)
Local Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 1544.10 kDa 
• Atom Count: 99250 
• Modelled Residue Count: 12872 
• Deposited Residue Count: 14142 
• Unique protein chains: 3

5ZVS

Structure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly

• PDB DOI: 10.2210/pdb5ZVS/pdb
• EM Map EMD-6968: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Grass carp reovirus
• Expression System: Ctenopharyngodon idella
• Mutation(s): No 


• Deposited: 2018-05-12 Released: 2018-07-04 
• Deposition Author(s): Liu, H., Fang, Q., Cheng, L.
• Funding Organization(s): Ministry of Science and Technology (China), National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly.

Wang, X., Zhang, F., Su, R., Li, X., Chen, W., Chen, Q., Yang, T., Wang, J., Liu, H., Fang, Q., Cheng, L.

(2018) Proc Natl Acad Sci U S A 115: 7344-7349

• PubMed: 29941585 
• DOI: 10.1073/pnas.1803885115
• Primary Citation of Related Structures:  
  5ZVS, 5ZVT


• PubMed Abstract: 
  

Most double-stranded RNA (dsRNA) viruses transcribe RNA plus strands within a common innermost capsid shell. This process requires coordinated efforts by RNA-dependent RNA polymerase (RdRp) together with other capsid proteins and genomic RNA. Here we report the near-atomic resolution structure of the RdRp protein VP2 in complex with its cofactor protein VP4 and genomic RNA within an aquareovirus capsid using 200-kV cryoelectron microscopy and symmetry-mismatch reconstruction. The structure of these capsid proteins enabled us to observe the elaborate nonicosahedral structure within the double-layered icosahedral capsid. Our structure shows that the RdRp complex is anchored at the inner surface of the capsid shell and interacts with genomic dsRNA and four of the five asymmetrically arranged N termini of the capsid shell proteins under the fivefold axis, implying roles for these N termini in virus assembly. The binding site of the RNA end at VP2 is different from the RNA cap binding site identified in the crystal structure of orthoreovirus RdRp λ3, although the structures of VP2 and λ3 are almost identical. A loop, which was thought to separate the RNA template and transcript, interacts with an apical domain of the capsid shell protein, suggesting a mechanism for regulating RdRp replication and transcription. A conserved nucleoside triphosphate binding site was localized in our RdRp cofactor protein VP4 structure, and interactions between the VP4 and the genomic RNA were identified.

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Organizational Affiliation: 

Technology Center for Protein Sciences, Tsinghua University, Beijing 100084, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP3	A, B, D [auth C], C [auth D], E, F, G, H, I, J	1214	Grass carp reovirus	Mutation(s): 0
UniProt
Find proteins for Q9E3V8 (Grass carp reovirus) Explore Q9E3V8  Go to UniProtKB:  Q9E3V8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VP2	K [auth 2]	1274	Grass carp reovirus	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for Q9E3V9 (Grass carp reovirus) Explore Q9E3V9  Go to UniProtKB:  Q9E3V9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative core protein NTPase/VP5	L [auth 4]	728	Grass carp reovirus	Mutation(s): 0
UniProt
Find proteins for Q8JU68 (Grass carp reovirus) Explore Q8JU68  Go to UniProtKB:  Q8JU68

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-05-12 
• Released Date: 2018-07-04 
Deposition Author(s): Liu, H., Fang, Q., Cheng, L.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	2016YFA0501100
Ministry of Science and Technology (China)	China	2015CB910104
National Natural Science Foundation of China	China	91530321
National Natural Science Foundation of China	China	31672693
National Natural Science Foundation of China	China	31570727

Revision History  

• Version 1.0: 2018-07-04
  Type: Initial release
  
• Version 1.1: 2018-07-25
  Changes: Data collection, Database references