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 

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Ligand Structure Quality Assessment 


This is version 1.2 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
PROBABLE ATP-DEPENDENT RNA HELICASE DDX58A687Homo 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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
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
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 
D [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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

  • Deposited Date: 2012-06-17 
  • Released Date: 2012-10-03 
  • Deposition Author(s): Luo, D., Pyle, A.M.

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