3OG8

Crystal structure of human RIG-I CTD bound to a 14-bp blunt-ended dsRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of RIG-I C-terminal domain bound to blunt-ended double-strand RNA without 5' triphosphate.

Lu, C.Ranjith-Kumar, C.T.Hao, L.Kao, C.C.Li, P.

(2011) Nucleic Acids Res 39: 1565-1575

  • DOI: 10.1093/nar/gkq974
  • Primary Citation of Related Structures:  
    3OG8

  • PubMed Abstract: 
  • RIG-I recognizes molecular patterns in viral RNA to regulate the induction of type I interferons. The C-terminal domain (CTD) of RIG-I exhibits high affinity for 5' triphosphate (ppp) dsRNA as well as blunt-ended dsRNA. Structures of RIG-I CTD bound ...

    RIG-I recognizes molecular patterns in viral RNA to regulate the induction of type I interferons. The C-terminal domain (CTD) of RIG-I exhibits high affinity for 5' triphosphate (ppp) dsRNA as well as blunt-ended dsRNA. Structures of RIG-I CTD bound to 5'-ppp dsRNA showed that RIG-I recognizes the termini of dsRNA and interacts with the ppp through electrostatic interactions. However, the structural basis for the recognition of non-phosphorylated dsRNA by RIG-I is not fully understood. Here, we show that RIG-I CTD binds blunt-ended dsRNA in a different orientation compared to 5' ppp dsRNA and interacts with both strands of the dsRNA. Overlapping sets of residues are involved in the recognition of blunt-ended dsRNA and 5' ppp dsRNA. Mutations at the RNA-binding surface affect RNA binding and signaling by RIG-I. These results provide the mechanistic basis for how RIG-I recognizes different RNA ligands.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DDX58AB128Homo sapiensMutation(s): 1 
Gene Names: DDX58
EC: 3.6.4.13
Find proteins for O95786 (Homo sapiens)
Explore O95786 
Go to UniProtKB:  O95786
NIH Common Fund Data Resources
PHAROS  O95786
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')C, D14N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download CCD File 
    A, B
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.40 Å
    • R-Value Free: 0.278 
    • R-Value Work: 0.217 
    • R-Value Observed: 0.217 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 36.99α = 90
    b = 70.3β = 90
    c = 125.54γ = 90
    Software Package:
    Software NamePurpose
    CrystalCleardata collection
    MOLREPphasing
    CNSrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    • Deposited Date: 2010-08-16 
    • Released Date: 2010-11-03 
    • Deposition Author(s): Li, P.

    Revision History 

    • Version 1.0: 2010-11-03
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance