2YKG

Structural insights into RNA recognition by RIG-I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural Insights Into RNA Recognition by Rig-I.

Luo, D.Ding, S.C.Vela, A.Kohlway, A.Lindenbach, B.D.Pyle, A.M.

(2011) Cell 147: 409

  • DOI: 10.1016/j.cell.2011.09.023
  • Primary Citation of Related Structures:  
    4BPB, 2YKG

  • PubMed Abstract: 
  • Intracellular RIG-I-like receptors (RLRs, including RIG-I, MDA-5, and LGP2) recognize viral RNAs as pathogen-associated molecular patterns (PAMPs) and initiate an antiviral immune response. To understand the molecular basis of this process, we determined the crystal structure of RIG-I in complex with double-stranded RNA (dsRNA) ...

    Intracellular RIG-I-like receptors (RLRs, including RIG-I, MDA-5, and LGP2) recognize viral RNAs as pathogen-associated molecular patterns (PAMPs) and initiate an antiviral immune response. To understand the molecular basis of this process, we determined the crystal structure of RIG-I in complex with double-stranded RNA (dsRNA). The dsRNA is sheathed within a network of protein domains that include a conserved "helicase" domain (regions HEL1 and HEL2), a specialized insertion domain (HEL2i), and a C-terminal regulatory domain (CTD). A V-shaped pincer connects HEL2 and the CTD by gripping an α-helical shaft that extends from HEL1. In this way, the pincer coordinates functions of all the domains and couples RNA binding with ATP hydrolysis. RIG-I falls within the Dicer-RIG-I clade of the superfamily 2 helicases, and this structure reveals complex interplay between motor domains, accessory mechanical domains, and RNA that has implications for understanding the nanomechanical function of this protein family and other ATPases more broadly.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROBABLE ATP-DEPENDENT RNA HELICASE DDX58 A696Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3'C, D10Homo sapiens
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SO4
    Query on SO4

    Download Ideal Coordinates CCD File 
    A
    SULFATE ION
    O4 S
    QAOWNCQODCNURD-UHFFFAOYSA-L
     Ligand Interaction
    ZN
    Query on ZN

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.50 Å
    • R-Value Free: 0.273 
    • R-Value Work: 0.220 
    • R-Value Observed: 0.223 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 47.618α = 90
    b = 76.208β = 90
    c = 219.825γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    • Deposited Date: 2011-05-27 
    • Released Date: 2011-10-26 
    • Deposition Author(s): Luo, D., Pyle, A.M.

    Revision History  (Full details and data files)

    • Version 1.0: 2011-10-26
      Type: Initial release