4A36

Structure of duck RIG-I helicase domain bound to 19-mer dsRNA and ATP transition state analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • 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
556Anas platyrhynchosMutation(s): 0 
Gene Names: RIG-I
Find proteins for D3TI84 (Anas platyrhynchos)
Go to UniProtKB:  D3TI84
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*GP*CP*AP*UP*GP*CP*GP*AP*CP*CP*UP*CP*UP*GP *UP*UP*UP*GP*A)-3'R,T19synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(*UP*CP*AP*AP*AP*CP*AP*GP*AP*GP*GP*UP*CP*GP *CP*AP*UP*GP*C)-3'S,U19synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AF3
Query on AF3

Download SDF File 
Download CCD File 
A, B
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.193 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 129.270α = 90.00
b = 129.270β = 90.00
c = 106.310γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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: 2015-05-20
    Type: Source and taxonomy
  • Version 1.3: 2019-04-03
    Type: Data collection, Other, Source and taxonomy