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- EMDB-0024: CryoEM structure of the MDA5-dsRNA filament in complex with ATP (... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0024 | |||||||||
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Title | CryoEM structure of the MDA5-dsRNA filament in complex with ATP (10 mM) | |||||||||
![]() | Final helical reconstruction map | |||||||||
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![]() | Protein-RNA complex / helical filament / ATPase / innate immune receptor / IMMUNE SYSTEM | |||||||||
Function / homology | ![]() MDA-5 signaling pathway / Ub-specific processing proteases / positive regulation of response to cytokine stimulus / pattern recognition receptor activity / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / positive regulation of interferon-alpha production / protein sumoylation / ribonucleoprotein complex binding ...MDA-5 signaling pathway / Ub-specific processing proteases / positive regulation of response to cytokine stimulus / pattern recognition receptor activity / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / positive regulation of interferon-alpha production / protein sumoylation / ribonucleoprotein complex binding / antiviral innate immune response / positive regulation of interferon-beta production / response to virus / cellular response to virus / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / double-stranded RNA binding / protein complex oligomerization / defense response to virus / RNA helicase activity / single-stranded RNA binding / RNA helicase / protein domain specific binding / innate immune response / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.87 Å | |||||||||
![]() | Yu Q / Qu K | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis. Authors: Qin Yu / Kun Qu / Yorgo Modis / ![]() Abstract: 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 ...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. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 5.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.9 KB 23.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.3 KB | Display | ![]() |
Images | ![]() | 158.4 KB | ||
Masks | ![]() | 42.9 MB | ![]() | |
Filedesc metadata | ![]() | 7.6 KB | ||
Others | ![]() ![]() | 12.3 MB 12.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gkmMC ![]() 0012C ![]() 0023C ![]() 0143C ![]() 0145C ![]() 4338C ![]() 4340C ![]() 4341C ![]() 6g19C ![]() 6g1sC ![]() 6g1xC ![]() 6gjzC ![]() 6gkhC ![]() 6h61C ![]() 6h66C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data #1: mouse MDA5-dsRNA filaments in complex with 10mM ATP [micrographs - single frame]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Final helical reconstruction map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_0024_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_0024_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : MDA5-dsRNA helical filament in complex with ATP
Entire | Name: MDA5-dsRNA helical filament in complex with ATP |
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Components |
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-Supramolecule #1: MDA5-dsRNA helical filament in complex with ATP
Supramolecule | Name: MDA5-dsRNA helical filament in complex with ATP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: Filaments formed in the presence of 10 mM ATP and frozen 7.5 min after addition of ATP |
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Molecular weight | Theoretical: 2.171 kDa/nm |
-Supramolecule #2: MDA5 bound to ATP
Supramolecule | Name: MDA5 bound to ATP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 Details: DExD/H-box helicase consisting of Hel1, Hel2, Hel2i, and pincer domains, followed by a C-terminal domain |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: Double-stranded RNA from bacteriophage Phi6
Supramolecule | Name: Double-stranded RNA from bacteriophage Phi6 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Interferon-induced helicase C domain-containing protein 1
Macromolecule | Name: Interferon-induced helicase C domain-containing protein 1 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 114.214477 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSIVCSAEDS FRNLILFFRP RLKMYIQVEP VLDHLIFLSA ETKEQILKKI NTCGNTSAAE LLLSTLEQGQ WPLGWTQMFV EALEHSGNP LAARYVKPTL TDLPSPSSET AHDECLHLLT LLQPTLVDKL LINDVLDTCF EKGLLTVEDR NRISAAGNSG N ESGVRELL ...String: MSIVCSAEDS FRNLILFFRP RLKMYIQVEP VLDHLIFLSA ETKEQILKKI NTCGNTSAAE LLLSTLEQGQ WPLGWTQMFV EALEHSGNP LAARYVKPTL TDLPSPSSET AHDECLHLLT LLQPTLVDKL LINDVLDTCF EKGLLTVEDR NRISAAGNSG N ESGVRELL RRIVQKENWF STFLDVLRQT GNDALFQELT GGGCPEDNTD LANSSHRDGP AANECLLPAV DESSLETEAW NV DDILPEA SCTDSSVTTE SDTSLAEGSV SCFDESLGHN SNMGRDSGTM GSDSDESVIQ TKRVSPEPEL QLRPYQMEVA QPA LDGKNI IICLPTGSGK TRVAVYITKD HLDKKKQASE SGKVIVLVNK VMLAEQLFRK EFNPYLKKWY RIIGLSGDTQ LKIS FPEVV KSYDVIISTA QILENSLLNL ESGDDDGVQL SDFSLIIIDE CHHTNKEAVY NNIMRRYLKQ KLRNNDLKKQ NKPAI PLPQ ILGLTASPGV GAAKKQSEAE KHILNICANL DAFTIKTVKE NLGQLKHQIK EPCKKFVIAD DTRENPFKEK LLEIMA SIQ TYCQKSPMSD FGTQHYEQWA IQMEKKAAKD GNRKDRVCAE HLRKYNEALQ INDTIRMIDA YSHLETFYTD EKEKKFA VL NDSKKSLKLD ETDEFLMNLF FDNKKMLKKL AENPKYENEK LIKLRNTILE QFTRSEESSR GIIFTKTRQS TYALSQWI M ENAKFAEVGV KAHHLIGAGH SSEVKPMTQT EQKEVISKFR TGEINLLIAT TVAEEGLDIK ECNIVIRYGL VTNEIAMVQ ARGRARADES TYVLVTSSGS GVTEREIVND FREKMMYKAI NRVQNMKPEE YAHKILELQV QSILEKKMKV KRSIAKQYND NPSLITLLC KNCSMLVCSG ENIHVIEKMH HVNMTPEFKG LYIVRENKAL QKKFADYQTN GEIICKCGQA WGTMMVHKGL D LPCLKIRN FVVNFKNNSP KKQYKKWVEL PIRFPDLDYS EYCLYSDED UniProtKB: Interferon-induced helicase C domain-containing protein 1 |
-Macromolecule #2: RNA (5'-R(P*CP*AP*AP*GP*CP*CP*GP*AP*GP*GP*AP*GP*AP*G)-3')
Macromolecule | Name: RNA (5'-R(P*CP*AP*AP*GP*CP*CP*GP*AP*GP*GP*AP*GP*AP*G)-3') type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 4.587852 KDa |
Sequence | String: CAAGCCGAGG AGAG |
-Macromolecule #3: RNA (5'-R(P*CP*UP*CP*UP*CP*CP*UP*CP*GP*GP*CP*UP*UP*G)-3')
Macromolecule | Name: RNA (5'-R(P*CP*UP*CP*UP*CP*CP*UP*CP*GP*GP*CP*UP*UP*G)-3') type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 4.35258 KDa |
Sequence | String: CUCUCCUCGG CUUG |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Concentration | 0.5 mg/mL | |||||||||||||||
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Buffer | pH: 7.7 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 25 mA | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | Samples were diluted twofold from 1 mg/ml to 0.5 mg/ml immediately prior to plunge freezing |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 30.24 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -3.1 µm / Nominal defocus min: -1.7 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 175 / Target criteria: Cross-correlation coefficient |
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Output model | ![]() PDB-6gkm: |