7JL1

Cryo-EM structure of RIG-I:dsRNA in complex with RIPLET PrySpry domain (monomer)


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases.

Kato, K.Ahmad, S.Zhu, Z.Young, J.M.Mu, X.Park, S.Malik, H.S.Hur, S.

(2021) Mol Cell 81: 599-613.e8

  • DOI: https://doi.org/10.1016/j.molcel.2020.11.047
  • Primary Citation of Related Structures:  
    7JL0, 7JL1, 7JL2, 7JL3, 7JL4

  • PubMed Abstract: 

    RNA helicases and E3 ubiquitin ligases mediate many critical functions in cells, but their actions have largely been studied in distinct biological contexts. Here, we uncover evolutionarily conserved rules of engagement between RNA helicases and tripartite motif (TRIM) E3 ligases that lead to their functional coordination in vertebrate innate immunity. Using cryoelectron microscopy and biochemistry, we show that RIG-I-like receptors (RLRs), viral RNA receptors with helicase domains, interact with their cognate TRIM/TRIM-like E3 ligases through similar epitopes in the helicase domains. Their interactions are avidity driven, restricting the actions of TRIM/TRIM-like proteins and consequent immune activation to RLR multimers. Mass spectrometry and phylogeny-guided biochemical analyses further reveal that similar rules of engagement may apply to diverse RNA helicases and TRIM/TRIM-like proteins. Our analyses suggest not only conserved substrates for TRIM proteins but also, unexpectedly, deep evolutionary connections between TRIM proteins and RNA helicases, linking ubiquitin and RNA biology throughout animal evolution.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antiviral innate immune response receptor RIG-I722Homo sapiensMutation(s): 0 
Gene Names: DDX58
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for O95786 (Homo sapiens)
Explore O95786 
Go to UniProtKB:  O95786
PHAROS:  O95786
GTEx:  ENSG00000107201 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95786
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF135D [auth B]184Homo sapiensMutation(s): 0 
Gene Names: RNF135L13
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IUD6 (Homo sapiens)
Explore Q8IUD6 
Go to UniProtKB:  Q8IUD6
PHAROS:  Q8IUD6
GTEx:  ENSG00000181481 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IUD6
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
dsRNA strand 1B [auth X]14Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
dsRNA strand 2C [auth Y]14Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2021-02-17
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references