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- EMDB-41060: Cryo-EM structure of DRH-1 helicase and C-terminal domain bound t... -

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Basic information

Entry
Database: EMDB / ID: EMD-41060
TitleCryo-EM structure of DRH-1 helicase and C-terminal domain bound to dsRNA
Map data
Sample
  • Complex: DRH-1 helicase and CTD bound to dsRNA
    • Protein or peptide: Dicer-related helicase
    • RNA: RNA (30-MER)
    • RNA: RNA (30-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordshelicase / 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
RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. ...RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dicer-related helicase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsConsalvo CD / Donelick HM / Shen PS / Bass BL
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM141262 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA260414 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI055434 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM133772
CitationJournal: 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
DepositionJun 14, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41060.png

Downloads & links

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Map

FileDownload / File: emd_41060.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 270.848 Å		1.06 Å/pix.
x 256 pix.
= 270.848 Å		1.06 Å/pix.
x 256 pix.
= 270.848 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.3121511 - 0.9675329
Average (Standard dev.)0.00011839055 (±0.018988043)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.848 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41060_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41060_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : DRH-1 helicase and CTD bound to dsRNA

EntireName: DRH-1 helicase and CTD bound to dsRNA
Components
  • Complex: DRH-1 helicase and CTD bound to dsRNA
    • Protein or peptide: Dicer-related helicase
    • RNA: RNA (30-MER)
    • RNA: RNA (30-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: DRH-1 helicase and CTD bound to dsRNA

SupramoleculeName: DRH-1 helicase and CTD bound to dsRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Dicer-related helicase

MacromoleculeName: Dicer-related helicase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 125.155383 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: RNA (30-MER)

MacromoleculeName: RNA (30-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.140017 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU

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Macromolecule #3: RNA (30-MER)

MacromoleculeName: RNA (30-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.831217 KDa
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: OTHER / Details: Ab Initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 362869
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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