8G7V | pdb_00008g7v

Cryo-EM structure of Riplet:RIG-I:dsRNA complex (end-inter)

  • Classification: Transferase/Hydrolase/RNA
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-02-17 Released: 2023-11-15 
  • Deposition Author(s): Wang, W., Pyle, A.M.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

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

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8G7V

This is version 1.4 of the entry. See complete history

Literature

The E3 ligase Riplet promotes RIG-I signaling independent of RIG-I oligomerization.

Wang, W.Gotte, B.Guo, R.Pyle, A.M.

(2023) Nat Commun 14: 7308-7308

  • DOI: https://doi.org/10.1038/s41467-023-42982-0
  • Primary Citation Related Structures: 
    8G7T, 8G7U, 8G7V

  • PubMed Abstract: 

    RIG-I is an essential innate immune receptor that responds to infection by RNA viruses. The RIG-I signaling cascade is mediated by a series of post-translational modifications, the most important of which is ubiquitination of the RIG-I Caspase Recruitment Domains (CARDs) by E3 ligase Riplet. This is required for interaction between RIG-I and its downstream adapter protein MAVS, but the mechanism of action remains unclear. Here we show that Riplet is required for RIG-I signaling in the presence of both short and long dsRNAs, establishing that Riplet activation does not depend upon RIG-I filament formation on long dsRNAs. Likewise, quantitative Riplet-RIG-I affinity measurements establish that Riplet interacts with RIG-I regardless of whether the receptor is bound to RNA. To understand this, we solved high-resolution cryo-EM structures of RIG-I/RNA/Riplet complexes, revealing molecular interfaces that control Riplet-mediated activation and enabling the formulation of a unified model for the role of Riplet in signaling.


  • Organizational Affiliation
    • Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06511, USA.

Macromolecule Content 

  • Total Structure Weight: 325.18 kDa 
  • Atom Count: 14,007 
  • Modeled Residue Count: 1,667 
  • Deposited Residue Count: 2,762 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Antiviral innate immune response receptor RIG-I
A, C
925Homo 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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF135
B, D
432Homo 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
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
p3dsRNA24aE [auth X]24Homo sapiens
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 4
MoleculeChains LengthOrganismImage
p3dsRNA24bF [auth Y]24Homo sapiens
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 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI131518

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Source and taxonomy
  • Version 1.2: 2024-05-29
    Changes: Database references, Structure summary
  • Version 1.3: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.4: 2025-05-28
    Changes: Data collection