5ZVS

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


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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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VP31214Grass carp reovirusMutation(s): 0 
UniProt
Find proteins for Q9E3V8 (Grass carp reovirus)
Explore Q9E3V8 
Go to UniProtKB:  Q9E3V8
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UniProt GroupQ9E3V8
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
VP2K [auth 2]1274Grass carp reovirusMutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for Q9E3V9 (Grass carp reovirus)
Explore Q9E3V9 
Go to UniProtKB:  Q9E3V9
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UniProt GroupQ9E3V9
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Putative core protein NTPase/VP5L [auth 4]728Grass carp reovirusMutation(s): 0 
UniProt
Find proteins for Q8JU68 (Grass carp reovirus)
Explore Q8JU68 
Go to UniProtKB:  Q8JU68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JU68
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0501100
Ministry of Science and Technology (China)China2015CB910104
National Natural Science Foundation of ChinaChina91530321
National Natural Science Foundation of ChinaChina31672693
National Natural Science Foundation of ChinaChina31570727

Revision History  (Full details and data files)

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