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 7BAH | pdb_00007bah

Structure of RIG-I CTD bound to OH-RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.224 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7BAH

This is version 1.2 of the entry. See complete history. 

Literature

A conserved isoleucine in the binding pocket of RIG-I controls immune tolerance to mitochondrial RNA.

de Regt, A.K., Anand, K., Ciupka, K., Bender, F., Gatterdam, K., Putschli, B., Fussholler, D., Hilbig, D., Kirchhoff, A., Hunkler, C., Wolter, S., Grunewald, A., Wallerath, C., Schuberth-Wagner, C., Ludwig, J., Paeschke, K., Bartok, E., Hagelueken, G., Hartmann, G., Zillinger, T., Geyer, M., Schlee, M.

(2023) Nucleic Acids Res 51: 11893-11910

  • DOI: https://doi.org/10.1093/nar/gkad835
  • Primary Citation Related Structures: 
    7BAH, 7BAI

  • PubMed Abstract: 

    RIG-I is a cytosolic receptor of viral RNA essential for the immune response to numerous RNA viruses. Accordingly, RIG-I must sensitively detect viral RNA yet tolerate abundant self-RNA species. The basic binding cleft and an aromatic amino acid of the RIG-I C-terminal domain(CTD) mediate high-affinity recognition of 5'triphosphorylated and 5'base-paired RNA(dsRNA). Here, we found that, while 5'unmodified hydroxyl(OH)-dsRNA demonstrated residual activation potential, 5'-monophosphate(5'p)-termini, present on most cellular RNAs, prevented RIG-I activation. Determination of CTD/dsRNA co-crystal structures and mutant activation studies revealed that the evolutionarily conserved I875 within the CTD sterically inhibits 5'p-dsRNA binding. RIG-I(I875A) was activated by both synthetic 5'p-dsRNA and endogenous long dsRNA within the polyA-rich fraction of total cellular RNA. RIG-I(I875A) specifically interacted with long, polyA-bearing, mitochondrial(mt) RNA, and depletion of mtRNA from total RNA abolished its activation. Altogether, our study demonstrates that avoidance of 5'p-RNA recognition is crucial to prevent mtRNA-triggered RIG-I-mediated autoinflammation.


  • Organizational Affiliation: 
    • Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany.

Macromolecule Content 

  • Total Structure Weight: 37.41 kDa 
  • Atom Count: 2,747 
  • Modeled Residue Count: 267 
  • Deposited Residue Count: 278 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Antiviral innate immune response receptor RIG-I
A, B
127Homo 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 nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*C)-3')
C, D
12synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.224 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.92α = 90
b = 81.92β = 90
c = 111.87γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyEXC2151-390873048

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2025-04-30
    Changes: Database references, Structure summary