5JC3

Crystal structure of chicken MDA5 with 5'p 10-mer dsRNA and ADP-Mg2+ at 2.6 A resolution (monoclinic form, twinned).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.271 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5.

Uchikawa, E.Lethier, M.Malet, H.Brunel, J.Gerlier, D.Cusack, S.

(2016) Mol.Cell 62: 586-602

  • DOI: 10.1016/j.molcel.2016.04.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • RIG-I and MDA5 sense virus-derived short 5'ppp blunt-ended or long dsRNA, respectively, causing interferon production. Non-signaling LGP2 appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. Co-crystal structures of c ...

    RIG-I and MDA5 sense virus-derived short 5'ppp blunt-ended or long dsRNA, respectively, causing interferon production. Non-signaling LGP2 appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. Co-crystal structures of chicken (ch) LGP2 with dsRNA display a fully or semi-closed conformation depending on the presence or absence of nucleotide. LGP2 caps blunt, 3' or 5' overhang dsRNA ends with 1 bp longer overall footprint than RIG-I. Structures of 1:1 and 2:1 complexes of chMDA5 with short dsRNA reveal head-to-head packing rather than the polar head-to-tail orientation described for long filaments. chLGP2 and chMDA5 make filaments with a similar axial repeat, although less co-operatively for chLGP2. Overall, LGP2 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. Functionally, RNA binding is required for LGP2-mediated enhancement of MDA5 activation. We propose that LGP2 end-binding may promote nucleation of MDA5 oligomerization on dsRNA.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; University Grenoble Alpes, Centre National de la Recherche Scientifique, EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Melanoma differentiation associated protein-5
A, B
701Gallus gallusMutation(s): 0 
Gene Names: MDA5
Find proteins for D9N195 (Gallus gallus)
Go to UniProtKB:  D9N195
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3')X,Y,C,D10synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.271 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.160α = 90.00
b = 138.700β = 109.47
c = 100.430γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilFrance322586

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Author supporting evidence, Data collection, Source and taxonomy