4GL2

Structural Basis for dsRNA duplex backbone recognition by MDA5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.557 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.276 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for dsRNA Recognition, Filament Formation, and Antiviral Signal Activation by MDA5.

Wu, B.Peisley, A.Richards, C.Yao, H.Zeng, X.Lin, C.Chu, F.Walz, T.Hur, S.

(2013) Cell 152: 276-289

  • DOI: 10.1016/j.cell.2012.11.048

  • PubMed Abstract: 
  • MDA5, a viral double-stranded RNA (dsRNA) receptor, shares sequence similarity and signaling pathways with RIG-I yet plays essential functions in antiviral immunity through distinct specificity for viral RNA. Revealing the molecular basis for the fun ...

    MDA5, a viral double-stranded RNA (dsRNA) receptor, shares sequence similarity and signaling pathways with RIG-I yet plays essential functions in antiviral immunity through distinct specificity for viral RNA. Revealing the molecular basis for the functional divergence, we report here the crystal structure of MDA5 bound to dsRNA, which shows how, using the same domain architecture, MDA5 recognizes the internal duplex structure, whereas RIG-I recognizes the terminus of dsRNA. We further show that MDA5 uses direct protein-protein contacts to stack along dsRNA in a head-to-tail arrangement, and that the signaling domain (tandem CARD), which decorates the outside of the core MDA5 filament, also has an intrinsic propensity to oligomerize into an elongated structure that activates the signaling adaptor, MAVS. These data support a model in which MDA5 uses long dsRNA as a signaling platform to cooperatively assemble the core filament, which in turn promotes stochastic assembly of the tandem CARD oligomers for signaling.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interferon-induced helicase C domain-containing protein 1
A, B
699Homo sapiensMutation(s): 0 
Gene Names: IFIH1 (MDA5, RH116)
EC: 3.6.4.13
Find proteins for Q9BYX4 (Homo sapiens)
Go to Gene View: IFIH1
Go to UniProtKB:  Q9BYX4
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*UP*CP*CP*GP*CP*GP*GP*CP*CP*CP*U)-3')C,E12N/A
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*GP*GP*GP*CP*CP*GP*CP*GP*GP*AP*U)-3')F,D12N/A
Small Molecules
Ligands 2 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
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.557 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.276 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.112α = 90.00
b = 154.748β = 90.00
c = 185.006γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
HKL-2000data reduction
APSdata collection
PHASESphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-08-13 
  • Released Date: 2013-01-09 
  • Deposition Author(s): Wu, B., Hur, S.

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-02-06
    Type: Database references