5H0R

RNA dependent RNA polymerase ,vp4,dsRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Near-Atomic Resolution Structure Determination of a Cypovirus Capsid and Polymerase Complex Using Cryo-EM at 200kV

Li, X.Zhou, N.Chen, W.Zhu, B.Wang, X.Xu, B.Wang, J.Liu, H.Cheng, L.

(2017) J Mol Biol 429: 79-87

  • DOI: https://doi.org/10.1016/j.jmb.2016.11.025
  • Primary Citation of Related Structures:  
    5H0R, 5H0S

  • PubMed Abstract: 

    Single-particle cryo-electron microscopy (cryo-EM) allows the high-resolution structural determination of biological assemblies in a near-native environment. However, all high-resolution (better than 3.5Å) cryo-EM structures reported to date were obtained by using 300kV transmission electron microscopes (TEMs). We report here the structures of a cypovirus capsid of 750-Å diameter at 3.3-Å resolution and of RNA-dependent RNA polymerase (RdRp) complexes within the capsid at 3.9-Å resolution using a 200-kV TEM. The newly resolved structure revealed conformational changes of two subdomains in the RdRp. These conformational changes, which were involved in RdRp's switch from non-transcribing to transcribing mode, suggest that the RdRp may facilitate the unwinding of genomic double-stranded RNA. The possibility of 3-Å resolution structural determinations for biological assemblies of relatively small sizes using cryo-EM at 200kV was discussed.


  • Organizational Affiliation

    College of Physics and Information Science, Synergetic Innovation Center for Quantum Effects and Applications, Hunan Normal University, Changsha, Hunan, 410081, China; Technology Center for Protein Sciences, Tsinghua University, Beijing, 100084, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-dependent RNA polymeraseA [auth F]1,225Bombyx mori cypovirus 1Mutation(s): 0 
Gene Names: RdRp
UniProt
Find proteins for A0A0S1LIW6 (Bombyx mori cytoplasmic polyhedrosis virus)
Explore A0A0S1LIW6 
Go to UniProtKB:  A0A0S1LIW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S1LIW6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VP4 proteinB [auth G]561Dendrolimus punctatus cypovirus 1Mutation(s): 0 
UniProt
Find proteins for Q80A92 (Dendrolimus punctatus cypovirus 1)
Explore Q80A92 
Go to UniProtKB:  Q80A92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ80A92
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (42-MER)C [auth H]42Cypovirus
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (42-MER)D [auth I]42Cypovirus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the National Research and Development Program of ChinaChina2016YFA0501103
he National Research and Development Program of ChinaChina2015CB910104
the National Natural Science Foundation of ChinaChina91530321
the National Natural Science Foundation of ChinaChina31570727
the National Natural Science Foundation of ChinaChina31570742

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references