3LRN

Crystal structure of human RIG-I CTD bound to a 14 bp GC 5' ppp dsRNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The Structural Basis of 5' Triphosphate Double-Stranded RNA Recognition by RIG-I C-Terminal Domain.

Lu, C., Xu, H., Ranjith-Kumar, C.T., Brooks, M.T., Hou, T.Y., Hu, F., Herr, A.B., Strong, R.K., Kao, C.C., Li, P.

(2010) Structure 18: 1032-1043

  • DOI: 10.1016/j.str.2010.05.007
  • Primary Citation of Related Structures:  
    3LRR, 3LRN

  • PubMed Abstract: 

    • RIG-I is a cytosolic sensor of viral RNA that plays crucial roles in the induction of type I interferons. The C-terminal domain (CTD) of RIG-I is responsible for the recognition of viral RNA with 5' triphosphate (ppp). However, the mechanism of viral RNA recognition by RIG-I is still not fully understood ...

    RIG-I is a cytosolic sensor of viral RNA that plays crucial roles in the induction of type I interferons. The C-terminal domain (CTD) of RIG-I is responsible for the recognition of viral RNA with 5' triphosphate (ppp). However, the mechanism of viral RNA recognition by RIG-I is still not fully understood. Here, we show that RIG-I CTD binds 5' ppp dsRNA or ssRNA, as well as blunt-ended dsRNA, and exhibits the highest affinity for 5' ppp dsRNA. Crystal structures of RIG-I CTD bound to 5' ppp dsRNA with GC- and AU-rich sequences revealed that RIG-I recognizes the termini of the dsRNA and interacts with the 5' ppp through extensive electrostatic interactions. Mutagenesis and RNA-binding studies demonstrated that similar binding surfaces are involved in the recognition of different forms of RNA. Mutations of key residues at the RNA-binding surface affected RIG-I signaling in cells.

    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
Probable ATP-dependent RNA helicase DDX58A, B121Homo sapiensMutation(s): 1 
Gene Names: DDX58, RIG-I
EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O95786 (Homo sapiens)
Explore O95786 
Go to UniProtKB:  O95786
PHAROS:  O95786
GTEx:  ENSG00000107201
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*(GTP)P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')C, D14N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN
    Download Ideal Coordinates CCD File 
    		 E [auth A], F [auth B]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.60 Å
    • R-Value Free: 0.282 
    • R-Value Work: 0.221 
    • R-Value Observed: 0.221 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 41.49α = 90
    b = 96.33β = 90
    c = 103.4γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    MOLREPphasing
    CNSrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report



    View more in-depth experimental data

    Entry History 

    Deposition Data

    • Deposited Date: 2010-02-11 
    • Released Date: 2010-06-02 
      • Deposition Author(s): Li, P.

    Revision History  (Full details and data files)

    • Version 1.0: 2010-06-02
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance