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: 3.70 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


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:  
    4A2P, 4A2Q, 4A2V, 4A2W, 4A2X, 4A36

  • 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 recruitment domains (CARDs), a DECH helicase, and a C-terminal domain (CTD) ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RETINOIC ACID INDUCIBLE PROTEIN IA, B556Anas platyrhynchosMutation(s): 0 
Gene Names: RIG-I
EC: 3.6.4.13
UniProt
Find proteins for D3TI84 (Anas platyrhynchos)
Explore D3TI84 
Go to UniProtKB:  D3TI84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3TI84
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*GP*CP*AP*UP*GP*CP*GP*AP*CP*CP*UP*CP*UP*GP *UP*UP*UP*GP*A)-3'C [auth R],
E [auth T]
19synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-R(*UP*CP*AP*AP*AP*CP*AP*GP*AP*GP*GP*UP*CP*GP *CP*AP*UP*GP*C)-3'D [auth S],
F [auth U]
19synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
AF3
Query on AF3

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B]
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.27α = 90
b = 129.27β = 90
c = 106.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references
  • Version 1.2: 2015-05-20
    Changes: Source and taxonomy
  • Version 1.3: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy