4GL2

Structural Basis for dsRNA duplex backbone recognition by MDA5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 

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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
  • Primary Citation of Related Structures:  
    4GL2

  • 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 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 ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interferon-induced helicase C domain-containing protein 1A, B699Homo sapiensMutation(s): 0 
Gene Names: IFIH1MDA5RH116
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYX4 (Homo sapiens)
Explore Q9BYX4 
Go to UniProtKB:  Q9BYX4
PHAROS:  Q9BYX4
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(*AP*UP*CP*CP*GP*CP*GP*GP*CP*CP*CP*U)-3')C, D [auth E]12N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*AP*GP*GP*GP*CP*CP*GP*CP*GP*GP*AP*U)-3')F [auth D], E [auth F]12N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
G [auth A], I [auth B]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth A], J [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.112α = 90
b = 154.748β = 90
c = 185.006γ = 90
Software Package:
Software NamePurpose
APSdata collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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