4A2X

Structure of duck RIG-I C-terminal domain (CTD) with 14-mer dSRNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


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

Literature

Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA.

Kowalinski, E., Lunardi, T., McCarthy, A.A., Louber, J., Brunel, J., Grigorov, B., Gerlier, D., Cusack, S.

(2011) Cell 147: 423-435

  • DOI: 10.1016/j.cell.2011.09.039
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • RIG-I is a key innate immune pattern-recognition receptor that triggers interferon expression upon detection of intracellular 5'triphosphate double-stranded RNA (5'ppp-dsRNA) of viral origin. RIG-I comprises N-terminal caspase activation and recruitm ...

    RIG-I is a key innate immune pattern-recognition receptor that triggers interferon expression upon detection of intracellular 5'triphosphate double-stranded RNA (5'ppp-dsRNA) of viral origin. RIG-I comprises N-terminal caspase activation and recruitment domains (CARDs), a DECH helicase, and a C-terminal domain (CTD). We present crystal structures of the ligand-free, autorepressed, and RNA-bound, activated states of RIG-I. Inactive RIG-I has an open conformation with the CARDs sequestered by a helical domain inserted between the two helicase moieties. ATP and dsRNA binding induce a major rearrangement to a closed conformation in which the helicase and CTD bind the blunt end 5'ppp-dsRNA with perfect complementarity but incompatibly with continued CARD binding. We propose that after initial binding of 5'ppp-dsRNA to the flexibly linked CTD, co-operative tight binding of ATP and RNA to the helicase domain liberates the CARDs for downstream signaling. These findings significantly advance our molecular understanding of the activation of innate immune signaling helicases.

    Organizational Affiliation: 

    European Molecular Biology Laboratory, Grenoble Outstation, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RETINOIC ACID INDUCIBLE PROTEIN I
A, B, C, D
131Anas platyrhynchosMutation(s): 0 
Gene Names: RIG-I
Find proteins for D3TI84 (Anas platyrhynchos)
Go to UniProtKB:  D3TI84
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*GP*GP*GP*AP*GP*AP*AP*CP*AP*AP*CP*GP*CP*GP)-3'L,N14synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(*CP*GP*CP*GP*UP*UP*GP*UP*UP*CP*UP*CP*CP*CP)-3'M,O14synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 216.020α = 90.00
b = 90.640β = 90.38
c = 62.960γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2011-10-26
    Type: Database references
  • Version 1.2: 2018-06-13
    Type: Data collection, Database references