3EQT

Crystal structure of human LGP2 C-terminal domain in complex with dsRNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


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


Literature

The RIG-I-like Receptor LGP2 Recognizes the Termini of Double-stranded RNA

Li, X., Ranjith-Kumar, C.T., Brooks, M.T., Dharmaiah, S., Herr, A.B., Kao, C., Li, P.

(2009) J Biol Chem 284: 13881-13891

  • DOI: 10.1074/jbc.M900818200
  • Primary Citation of Related Structures:  
    3EQT

  • PubMed Abstract: 

    • The RIG-I-like receptors (RLRs), RIG-I and MDA5, recognize single-stranded RNA with 5' triphosphates and double-stranded RNA (dsRNA) to initiate innate antiviral immune responses. LGP2, a homolog of RIG-I and MDA5 that lacks signaling capability, regulates the signaling of the RLRs ...

    The RIG-I-like receptors (RLRs), RIG-I and MDA5, recognize single-stranded RNA with 5' triphosphates and double-stranded RNA (dsRNA) to initiate innate antiviral immune responses. LGP2, a homolog of RIG-I and MDA5 that lacks signaling capability, regulates the signaling of the RLRs. To establish the structural basis of dsRNA recognition by the RLRs, we have determined the 2.0-A resolution crystal structure of human LGP2 C-terminal domain bound to an 8-bp dsRNA. Two LGP2 C-terminal domain molecules bind to the termini of dsRNA with minimal contacts between the protein molecules. Gel filtration chromatography and analytical ultracentrifugation demonstrated that LGP2 binds blunt-ended dsRNA of different lengths, forming complexes with 2:1 stoichiometry. dsRNA with protruding termini bind LGP2 and RIG-I weakly and do not stimulate the activation of RIG-I efficiently in cells. Surprisingly, full-length LGP2 containing mutations that abolish dsRNA binding retained the ability to inhibit RIG-I signaling.

    Organizational Affiliation: 

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



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DHX58 A, B145Homo sapiensMutation(s): 0 
Gene Names: D11LGP2E, DHX58, LGP2
EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
Find proteins for Q96C10 (Homo sapiens)
Explore Q96C10 
Go to UniProtKB:  Q96C10
NIH Common Fund Data Resources
PHAROS:  Q96C10
GTEx:  ENSG00000108771
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(*GP*CP*GP*CP*GP*CP*GP*C)-3'C, D8N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN
    Download Ideal Coordinates CCD File 
    A, B
    		ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.254 
    • R-Value Work: 0.213 
    • R-Value Observed: 0.214 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 116.458α = 90
    b = 54.191β = 97.26
    c = 67.203γ = 90
    Software Package:
    Software NamePurpose
    CrystalCleardata 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: 2008-10-01 
    • Released Date: 2009-03-10 
      • Deposition Author(s): Li, P., Li, X.

    Revision History  (Full details and data files)

    • Version 1.0: 2009-03-10
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance