4AY2

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

• PDB DOI: https://doi.org/10.2210/pdb4AY2/pdb
• NAKB: 4AY2

• Classification: HYDROLASE/RNA
• Organism(s): Homo sapiens
• Mutation(s): No 


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

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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 

Starting Model: experimental

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

• PubMed: 23022350 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 85.78 kDa 
• Atom Count: 5,542 
• Modelled Residue Count: 648 
• Deposited Residue Count: 707 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE ATP-DEPENDENT RNA HELICASE DDX58	A	687	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Length	Organism	Image
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]	20	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 47.745	α = 90
b = 76.156	β = 90
c = 221.222	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.4: 2024-10-09
  Changes: Structure summary