Crystal structure of RIG-I helicase-RD in complex with 24-mer blunt-end hairpin RNA

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I.

Devarkar, S.C.Wang, C.Miller, M.T.Ramanathan, A.Jiang, F.Khan, A.G.Patel, S.S.Marcotrigiano, J.

(2016) Proc Natl Acad Sci U S A 113: 596-601

  • DOI: https://doi.org/10.1073/pnas.1515152113
  • Primary Citation of Related Structures:  
    5F98, 5F9F, 5F9H

  • PubMed Abstract: 

    RNAs with 5'-triphosphate (ppp) are detected in the cytoplasm principally by the innate immune receptor Retinoic Acid Inducible Gene-I (RIG-I), whose activation triggers a Type I IFN response. It is thought that self RNAs like mRNAs are not recognized by RIG-I because 5'ppp is capped by the addition of a 7-methyl guanosine (m7G) (Cap-0) and a 2'-O-methyl (2'-OMe) group to the 5'-end nucleotide ribose (Cap-1). Here we provide structural and mechanistic basis for exact roles of capping and 2'-O-methylation in evading RIG-I recognition. Surprisingly, Cap-0 and 5'ppp double-stranded (ds) RNAs bind to RIG-I with nearly identical Kd values and activate RIG-I's ATPase and cellular signaling response to similar extents. On the other hand, Cap-0 and 5'ppp single-stranded RNAs did not bind RIG-I and are signaling inactive. Three crystal structures of RIG-I complexes with dsRNAs bearing 5'OH, 5'ppp, and Cap-0 show that RIG-I can accommodate the m7G cap in a cavity created through conformational changes in the helicase-motif IVa without perturbing the ppp interactions. In contrast, Cap-1 modifications abrogate RIG-I signaling through a mechanism involving the H830 residue, which we show is crucial for discriminating between Cap-0 and Cap-1 RNAs. Furthermore, m7G capping works synergistically with 2'-O-methylation to weaken RNA affinity by 200-fold and lower ATPase activity. Interestingly, a single H830A mutation restores both high-affinity binding and signaling activity with 2'-O-methylated dsRNAs. Our work provides new structural insights into the mechanisms of host and viral immune evasion from RIG-I, explaining the complexity of cap structures over evolution.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854;


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX58
A, C, E, G, I
A, C, E, G, I, K
695Homo sapiensMutation(s): 0 
Gene Names: DDX58
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
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
B, D, F, H, J
B, D, F, H, J, L
24synthetic construct
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ETF

Download Ideal Coordinates CCD File 
CA [auth G],
NA [auth K],
O [auth A],
Y [auth E]
C2 H3 F3 O
Query on BU3

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth G]
EA [auth G]
FA [auth G]
KA [auth I]
AA [auth E],
DA [auth G],
EA [auth G],
FA [auth G],
KA [auth I],
OA [auth K],
P [auth A],
Q [auth A],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
Z [auth E]
C4 H10 O2
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth G]
HA [auth I]
LA [auth K]
M [auth A]
R [auth C]
BA [auth G],
HA [auth I],
LA [auth K],
M [auth A],
R [auth C],
X [auth E]
Query on MG

Download Ideal Coordinates CCD File 
GA [auth H]
IA [auth I]
JA [auth I]
MA [auth K]
N [auth A]
GA [auth H],
IA [auth I],
JA [auth I],
MA [auth K],
N [auth A],
S [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.524α = 90
b = 174.252β = 90
c = 308.288γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-01-20
    Changes: Database references, Structure summary
  • Version 1.2: 2016-01-27
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description