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TitleCryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis.
Journal, issue, pagesMol. Cell, Vol. 72, Issue 6, Page 999-1012.e6, Year 2018
Publish dateDec 20, 2018
AuthorsQin Yu / Kun Qu / Yorgo Modis /
PubMed AbstractDouble-stranded RNA (dsRNA) is a potent proinflammatory signature of viral infection. Long cytosolic dsRNA is recognized by MDA5. The cooperative assembly of MDA5 into helical filaments on dsRNA ...Double-stranded RNA (dsRNA) is a potent proinflammatory signature of viral infection. Long cytosolic dsRNA is recognized by MDA5. The cooperative assembly of MDA5 into helical filaments on dsRNA nucleates the assembly of a multiprotein type I interferon signaling platform. Here, we determined cryoelectron microscopy (cryo-EM) structures of MDA5-dsRNA filaments with different helical twists and bound nucleotide analogs at resolutions sufficient to build and refine atomic models. The structures identify the filament-forming interfaces, which encode the dsRNA binding cooperativity and length specificity of MDA5. The predominantly hydrophobic interface contacts confer flexibility, reflected in the variable helical twist within filaments. Mutation of filament-forming residues can result in loss or gain of signaling activity. Each MDA5 molecule spans 14 or 15 RNA base pairs, depending on the twist. Variations in twist also correlate with variations in the occupancy and type of nucleotide in the active site, providing insights on how ATP hydrolysis contributes to MDA5-dsRNA recognition.
External linksPubMed:30449722 / Publisher's page
KeywordsAdenosine Triphosphate / Cryoelectron Microscopy / HEK293 Cells / Humans / Hydrolysis / Hydrophobic and Hydrophilic Interactions / IFIH1 protein, human / Ifih1 protein, mouse / Interferon-Induced Helicase, IFIH1 / Interferon-beta / Molecular Docking Simulation / Mutation / Nucleic Acid Conformation / Protein Conformation / RNA, Double-Stranded / Signal Transduction / Structure-Activity Relationship / IMMUNE SYSTEM / Protein-RNA complex / helical filament / ATPase / innate immune receptor
MethodsEM (helical sym.)
Resolution3.68 - 4.16 A
Structure data

EMDB-0012:
CryoEM structure of the MDA5-dsRNA filament in complex with AMPPNP

EMDB-0023:
CryoEM structure of the MDA5-dsRNA filament in complex with ADP-AlF4

EMDB-0024:
CryoEM structure of the MDA5-dsRNA filament in complex with ATP (10 mM)

EMDB-0143:
CryoEM structure of the MDA5-dsRNA filament with 89 degree twist and without nucleotide

EMDB-0145:
CryoEM structure of the MDA5-dsRNA filament with 93 degree twist and without nucleotide

EMDB-4338:
CryoEM structure of the MDA5-dsRNA filament with 74-degree helical twist

EMDB-4340:
CryoEM structure of the MDA5-dsRNA filament with 87-degree helical twist

EMDB-4341:
CryoEM structure of the MDA5-dsRNA filament with 91-degree helical twist

PDB-6g19:
CryoEM structure of the MDA5-dsRNA filament with 74-degree helical twist

PDB-6g1s:
CryoEM structure of the MDA5-dsRNA filament with 87-degree helical twist

PDB-6g1x:
CryoEM structure of the MDA5-dsRNA filament with 91-degree helical twist

PDB-6gjz:
CryoEM structure of the MDA5-dsRNA filament in complex with AMPPNP

PDB-6gkh:
CryoEM structure of the MDA5-dsRNA filament in complex with ADP-AlF4

PDB-6gkm:
CryoEM structure of the MDA5-dsRNA filament in complex with ATP (10 mM)

PDB-6h61:
CryoEM structure of the MDA5-dsRNA filament with 89 degree twist and without nucleotide

PDB-6h66:
CryoEM structure of the MDA5-dsRNA filament with 93 degree twist and without nucleotide

Chemicals

ChemComp-ZN:
ZINC ION / Zinc

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

ChemComp-MG:
MAGNESIUM ION / Magnesium

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

Source
  • mus musculus (house mouse)
  • Pseudomonas savastanoi pv. phaseolicola (bacteria)
  • pseudomonas phage phi6 (bacteriophage)

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