4AY2

Capturing 5' tri-phosphorylated RNA duplex by RIG-I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Visualizing the Determinants of Viral RNA Recognition by Innate Immune Sensor Rig-I.

Luo, D.Kohlway, A.Vela, A.Pyle, A.M.

(2012) Structure 20: 1983

  • DOI: https://doi.org/10.1016/j.str.2012.08.029
  • Primary Citation of Related Structures:  
    4AY2

  • PubMed Abstract: 

    Retinoic acid inducible gene-I (RIG-I) is a key intracellular immune receptor for pathogenic RNAs, particularly from RNA viruses. Here, we report the crystal structure of human RIG-I bound to a 5' triphosphorylated RNA hairpin and ADP nucleotide at 2.8 Å resolution. The RNA ligand contains all structural features that are essential for optimal recognition by RIG-I, as it mimics the panhandle-like signatures within the genome of negative-stranded RNA viruses. RIG-I adopts an intermediate, semiclosed conformation in this product state of ATP hydrolysis. The structure of this complex allows us to visualize the first steps in RIG-I recognition and activation upon viral infection.


  • Organizational Affiliation

    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROBABLE ATP-DEPENDENT RNA HELICASE DDX58687Homo sapiensMutation(s): 0 
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

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-R-PPP(GP*GP*CP*GP*CP*GP*GP*CP*UP*UP*CP*GP*GP*CP *CP*GP*CP*GP*CP*C)-3'B [auth C]20N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.745α = 90
b = 76.156β = 90
c = 221.222γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2012-11-21
    Changes: Database references
  • Version 1.2: 2012-11-28
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description