3ZD7

Snapshot 3 of RIG-I scanning on RNA duplex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


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


Literature

Defining the Functional Determinants for RNA Surveillance by Rig-I.

Kohlway, A., Luo, D., Rawling, D.C., Ding, S.C., Pyle, A.M.

(2013) EMBO Rep 14: 772

  • DOI: 10.1038/embor.2013.108
  • Primary Citation of Related Structures:  
    3ZD6, 3ZD7

  • PubMed Abstract: 

    • Retinoic acid-inducible gene-I (RIG-I) is an intracellular RNA sensor that activates the innate immune machinery in response to infection by RNA viruses. Here, we report the crystal structure of distinct conformations of a RIG-I:dsRNA complex, which shows that HEL2i-mediated scanning allows RIG-I to sense the length of RNA targets ...

    Retinoic acid-inducible gene-I (RIG-I) is an intracellular RNA sensor that activates the innate immune machinery in response to infection by RNA viruses. Here, we report the crystal structure of distinct conformations of a RIG-I:dsRNA complex, which shows that HEL2i-mediated scanning allows RIG-I to sense the length of RNA targets. To understand the implications of HEL2i scanning for catalytic activity and signalling by RIG-I, we examined its ATPase activity when stimulated by duplex RNAs of varying lengths and 5' composition. We identified a minimal RNA duplex that binds one RIG-I molecule, stimulates robust ATPase activity, and elicits a RIG-I-mediated interferon response in cells. Our results reveal that the minimal functional unit of the RIG-I:RNA complex is a monomer that binds at the terminus of a duplex RNA substrate. This behaviour is markedly different from the RIG-I paralog melanoma differentiation-associated gene 5 (MDA5), which forms cooperative filaments.

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry.



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
GTEx:  ENSG00000107201
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA DUPLEXC, D10synthetic construct
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP
    Query on ADP
    Download Ideal Coordinates CCD File 
    A
    		ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N    		 Ligand Interaction
    ZN
    Query on ZN
    Download Ideal Coordinates CCD File 
    A
    		ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N    		 Ligand Interaction
    MG
    Query on MG
    Download Ideal Coordinates CCD File 
    A
    		MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.50 Å
    • R-Value Free: 0.288 
    • R-Value Work: 0.229 
    • R-Value Observed: 0.232 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 48.252α = 90
    b = 75.996β = 90
    c = 207.279γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    PHASERphasing

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    • Deposited Date: 2012-11-25 
    • Released Date: 2013-08-07 
      • Deposition Author(s): Luo, D., Pyle, A.M.

    Revision History  (Full details and data files)

    • Version 1.0: 2013-08-07
      Type: Initial release
    • Version 1.1: 2013-09-11
      Changes: Database references