7JL0

Cryo-EM structure of MDA5-dsRNA in complex with TRIM65 PSpry domain (Monomer)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1016/j.molcel.2020.11.047
  • Primary Citation of Related Structures:  
    7JL3, 7JL4, 7JL1, 7JL2, 7JL0

  • 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 ...

    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. Electronic address: sun.hur@crystal.harvard.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon-induced helicase C domain-containing protein 1 A739Homo sapiensMutation(s): 0 
Gene Names: IFIH1MDA5RH116
EC: 3.6.4.13
Find proteins for Q9BYX4 (Homo sapiens)
Explore Q9BYX4 
Go to UniProtKB:  Q9BYX4
NIH Common Fund Data Resources
PHAROS:  Q9BYX4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Tripartite motif-containing protein 65 B191Homo sapiensMutation(s): 0 
Gene Names: TRIM65
Find proteins for Q6PJ69 (Homo sapiens)
Explore Q6PJ69 
Go to UniProtKB:  Q6PJ69
NIH Common Fund Data Resources
PHAROS:  Q6PJ69
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*GP*AP*CP*UP*GP*AP*CP*UP*GP*AP*CP*UP*GP*A)-3')X14Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(P*UP*CP*AP*GP*UP*CP*AP*GP*UP*CP*AP*GP*UP*C)-3')Y14Homo sapiens
      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ADP
      Query on ADP

      Download Ideal Coordinates CCD File 
      A
      ADENOSINE-5'-DIPHOSPHATE
      C10 H15 N5 O10 P2
      XTWYTFMLZFPYCI-KQYNXXCUSA-N
       Ligand Interaction
      ALF
      Query on ALF

      Download Ideal Coordinates CCD File 
      A
      TETRAFLUOROALUMINATE ION
      Al F4
      UYOMQIYKOOHAMK-UHFFFAOYSA-J
       Ligand Interaction
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      A
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      A
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: ELECTRON MICROSCOPY
      • Resolution: 4.30 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