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- EMDB-0145: CryoEM structure of the MDA5-dsRNA filament with 93 degree twist ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0145 | |||||||||
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Title | CryoEM structure of the MDA5-dsRNA filament with 93 degree twist and without nucleotide | |||||||||
![]() | cryoEM reconstruction map | |||||||||
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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 / antiviral innate immune response / protein sumoylation / positive regulation of interferon-alpha production ...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 / antiviral innate immune response / protein sumoylation / positive regulation of interferon-alpha production / ribonucleoprotein complex binding / 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: 4.16 Å | |||||||||
![]() | Yu Q / Qu K / Modis Y | |||||||||
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 | ![]() | 5.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.8 KB 23.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.7 KB | Display | ![]() |
Images | ![]() | 166.9 KB | ||
Masks | ![]() | 47.6 MB | ![]() | |
Others | ![]() ![]() | 11.5 MB 11.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 376.4 KB | Display | ![]() |
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Full document | ![]() | 375.5 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6h66MC ![]() 0012C ![]() 0023C ![]() 0024C ![]() 0143C ![]() 4338C ![]() 4340C ![]() 4341C ![]() 6g19C ![]() 6g1sC ![]() 6g1xC ![]() 6gjzC ![]() 6gkhC ![]() 6gkmC ![]() 6h61C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data #1: Unaligned multi-frame movies of mouse MDA5-dsRNA filaments without nucleotide [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryoEM reconstruction map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_0145_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_0145_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 without nucleotide
Entire | Name: MDA5-dsRNA helical filament without nucleotide |
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Components |
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-Supramolecule #1: MDA5-dsRNA helical filament without nucleotide
Supramolecule | Name: MDA5-dsRNA helical filament without nucleotide / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Filaments formed without nucleotide |
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Molecular weight | Theoretical: 2.23 kDa/nm |
-Supramolecule #2: MDA5 (IFIH1)
Supramolecule | Name: MDA5 (IFIH1) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 Details: RIG-I-like Superfamily 2 (SF2) RNA helicase consisting of Hel1, Hel2, Hel2i, and pincer domains, followed by a C-terminal domain |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Supramolecule #3: Double-stranded RNA from bacteriophage Phi6, generated by n vitro...
Supramolecule | Name: Double-stranded RNA from bacteriophage Phi6, generated by n vitro translation 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 |
-Macromolecule #2: RNA (5'-R(P*UP*CP*CP*AP*UP*GP*CP*GP*CP*AP*UP*GP*AP*CP*G)-3')
Macromolecule | Name: RNA (5'-R(P*UP*CP*CP*AP*UP*GP*CP*GP*CP*AP*UP*GP*AP*CP*G)-3') type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 4.767889 KDa |
Sequence | String: UCCAUGCGCA UGACG |
-Macromolecule #3: RNA (5'-R(P*CP*GP*UP*CP*AP*UP*GP*CP*GP*CP*AP*UP*GP*GP*A)-3')
Macromolecule | Name: RNA (5'-R(P*CP*GP*UP*CP*AP*UP*GP*CP*GP*CP*AP*UP*GP*GP*A)-3') type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 4.807914 KDa |
Sequence | String: CGUCAUGCGC AUGGA |
-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 |
-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 | ||||||||||||
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 / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 27.0 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: -2.7 µm / Nominal defocus min: -1.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |