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Yorodumi- PDB-8t5s: Cryo-EM structure of DRH-1 helicase and C-terminal domain bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8t5s | |||||||||||||||
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Title | Cryo-EM structure of DRH-1 helicase and C-terminal domain bound to dsRNA | |||||||||||||||
Components |
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Keywords | ANTIVIRAL PROTEIN/RNA / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||
Authors | Consalvo, C.D. / Donelick, H.M. / Shen, P.S. / Bass, B.L. | |||||||||||||||
Funding support | United States, 4items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t5s.cif.gz | 192.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t5s.ent.gz | 140.3 KB | Display | PDB format |
PDBx/mmJSON format | 8t5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/8t5s ftp://data.pdbj.org/pub/pdb/validation_reports/t5/8t5s | HTTPS FTP |
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-Related structure data
Related structure data | 41060MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 125155.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: drh-1, CELE_F15B10.2, F15B10.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G5EDI8 |
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-RNA chain , 2 types, 2 molecules CB
#2: RNA chain | Mass: 9140.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: RNA chain | Mass: 9831.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 3 molecules
#4: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-ADP / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DRH-1 helicase and CTD bound to dsRNA / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 100 nm |
Image recording | Electron dose: 38 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 362869 / Symmetry type: POINT |