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Yorodumi- EMDB-41060: Cryo-EM structure of DRH-1 helicase and C-terminal domain bound t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41060 | |||||||||||||||
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Title | Cryo-EM structure of DRH-1 helicase and C-terminal domain bound to dsRNA | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | helicase / RLR / RIG-I-like Receptor / ATPase / dsRNA / ANTIVIRAL PROTEIN-RNA complex | |||||||||||||||
Function / homology | Function and homology information Ub-specific processing proteases / regulatory ncRNA-mediated post-transcriptional gene silencing / helicase activity / nucleic acid binding / innate immune response / ATP binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Caenorhabditis elegans (invertebrata) / synthetic construct (others) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||
Authors | Consalvo CD / Donelick HM / Shen PS / Bass BL | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Elife / Year: 2024 Title: Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. Authors: Claudia D Consalvo / Adedeji M Aderounmu / Helen M Donelick / P Joseph Aruscavage / Debra M Eckert / Peter S Shen / Brenda L Bass / Abstract: Invertebrates use the endoribonuclease Dicer to cleave viral dsRNA during antiviral defense, while vertebrates use RIG-I-like Receptors (RLRs), which bind viral dsRNA to trigger an interferon ...Invertebrates use the endoribonuclease Dicer to cleave viral dsRNA during antiviral defense, while vertebrates use RIG-I-like Receptors (RLRs), which bind viral dsRNA to trigger an interferon response. While some invertebrate Dicers act alone during antiviral defense, Dicer acts in a complex with a dsRNA binding protein called RDE-4, and an RLR ortholog called DRH-1. We used biochemical and structural techniques to provide mechanistic insight into how these proteins function together. We found RDE-4 is important for ATP-independent and ATP-dependent cleavage reactions, while helicase domains of both DCR-1 and DRH-1 contribute to ATP-dependent cleavage. DRH-1 plays the dominant role in ATP hydrolysis, and like mammalian RLRs, has an N-terminal domain that functions in autoinhibition. A cryo-EM structure indicates DRH-1 interacts with DCR-1's helicase domain, suggesting this interaction relieves autoinhibition. Our study unravels the mechanistic basis of the collaboration between two helicases from typically distinct innate immune defense pathways. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41060.map.gz | 32.4 MB | EMDB map data format | |
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Header (meta data) | emd-41060-v30.xml emd-41060.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41060_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_41060.png | 21.3 KB | ||
Filedesc metadata | emd-41060.cif.gz | 6.4 KB | ||
Others | emd_41060_half_map_1.map.gz emd_41060_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41060 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41060 | HTTPS FTP |
-Validation report
Summary document | emd_41060_validation.pdf.gz | 841.1 KB | Display | EMDB validaton report |
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Full document | emd_41060_full_validation.pdf.gz | 840.6 KB | Display | |
Data in XML | emd_41060_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | emd_41060_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41060 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41060 | HTTPS FTP |
-Related structure data
Related structure data | 8t5sMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41060.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.058 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41060_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41060_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : DRH-1 helicase and CTD bound to dsRNA
Entire | Name: DRH-1 helicase and CTD bound to dsRNA |
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Components |
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-Supramolecule #1: DRH-1 helicase and CTD bound to dsRNA
Supramolecule | Name: DRH-1 helicase and CTD bound to dsRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
-Macromolecule #1: Dicer-related helicase
Macromolecule | Name: Dicer-related helicase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Molecular weight | Theoretical: 125.155383 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTRSPLEVL FQGPMRKKQC SSILSLYDKE IILCLEPIYR DPEKGDGFS ELLPLGRIDE LKIQSENAQE FSKQLYHDLK NSILSNADDE RLYKDIMTYL QTYLPKCTVH KLLNCSNREV K LSDFHYIL ...String: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTRSPLEVL FQGPMRKKQC SSILSLYDKE IILCLEPIYR DPEKGDGFS ELLPLGRIDE LKIQSENAQE FSKQLYHDLK NSILSNADDE RLYKDIMTYL QTYLPKCTVH KLLNCSNREV K LSDFHYIL DHFEGFLRFI EPKVVLAYLD SYPQYIDAVA VLRKEIERNE EDNQDSDFIK KLILRTVPLL GEQAVYDIMY TI SEKSSNN LDVEAKQFIA KVLRLKNDGF LRFYQIINAS RRQLNGRIYI CPVHESATEM MVYLGTAALN TNRYRMINIR VDN IVQENS TPRLVIESVR QRIHRQRQLC LRNYQEELCQ VALQGKNTIV TAPTGSGKTV IAANIIKEHF ESRSSEGKRF KALF MTPNS MILNQQAASI SSYLDHVYHT QIIQGSDNVP TRNVIQSKDL IVATPQMIVN LCNEHRNSLD DESRLDQFFL STFTI IFFD ECHNTVKNSP YSNIMREYHY LKNMGNMPEG HSLPQIIGLT ASLGTGDKND CLQVRNYIAG LCASMDVKDL SIVKDN LEE LRGYSPIVPD KVLLCERSTD GPIGMFTNRL TLMMQEVEGL IRTALRNEHI GIEQRRQIET TERDFRPDSS FLDPPAD KE HAGYQNWVCN QMNLVSGTSF RETGTRTIIN EALDVLKECF CTLSYNINFH PEVALNYLKD EMEYRTPNFT VNMIRIWE R YHNQLVGTGS AENPMISKTV QYIVEQNLQR ADSRTIIFVR TRYEATILNK VLNSNEELLM LGIKSEWMSG LNKSTASSA DISASKQKQM EKLKMFADGE IRILVSTSVA EEGLDVPECS LVIKYNYATN EIAHVQRRGR GRALNSECVL ITNSIALRDQ ESNNRDKES LMSETISLIQ NSPAEFRKCV DEESNKIWPR ILREDTDKAQ KIEEQINRNI VYKIICKKCE AILCTSKDIR S RNTQYLVC DPGFWSLVRK TRLTDEQQAL IKYNATGSIN CRRENCGLKL GQLIEVNTVD LPCLSALSIV LLVEGTDKRI IV KKWKNIL DKYFTPTEIR QLDVQTMRDA DQARTPMVFE HHANGEVVNL IREA UniProtKB: Dicer-related helicase |
-Macromolecule #2: RNA (30-MER)
Macromolecule | Name: RNA (30-MER) / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 9.140017 KDa |
Sequence | String: UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU |
-Macromolecule #3: RNA (30-MER)
Macromolecule | Name: RNA (30-MER) / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 9.831217 KDa |
Sequence | String: AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA |
-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: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.1 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |