+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41785 | |||||||||
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Title | DdmD dimer in complex with ssDNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DdmD / helicase / nuclease / IMMUNE SYSTEM / IMMUNE SYSTEM-DNA complex | |||||||||
Function / homology | Helicase/UvrB N-terminal domain-containing protein Function and homology information | |||||||||
Biological species | Vibrio cholerae (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 Å | |||||||||
Authors | Bravo JPK / Taylor DW | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nature / Year: 2024 Title: Plasmid targeting and destruction by the DdmDE bacterial defence system. Authors: Jack P K Bravo / Delisa A Ramos / Rodrigo Fregoso Ocampo / Caiden Ingram / David W Taylor / Abstract: Although eukaryotic Argonautes have a pivotal role in post-transcriptional gene regulation through nucleic acid cleavage, some short prokaryotic Argonaute variants (pAgos) rely on auxiliary nuclease ...Although eukaryotic Argonautes have a pivotal role in post-transcriptional gene regulation through nucleic acid cleavage, some short prokaryotic Argonaute variants (pAgos) rely on auxiliary nuclease factors for efficient foreign DNA degradation. Here we reveal the activation pathway of the DNA defence module DdmDE system, which rapidly eliminates small, multicopy plasmids from the Vibrio cholerae seventh pandemic strain (7PET). Through a combination of cryo-electron microscopy, biochemistry and in vivo plasmid clearance assays, we demonstrate that DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo with a distinctive insertion domain. We observe that the helicase-nuclease DdmD transitions from an autoinhibited, dimeric complex to a monomeric state upon loading of single-stranded DNA targets. Furthermore, the complete structure of the DdmDE-guide-target handover complex provides a comprehensive view into how DNA recognition triggers processive plasmid destruction. Our work establishes a mechanistic foundation for how pAgos utilize ancillary factors to achieve plasmid clearance, and provides insights into anti-plasmid immunity in bacteria. | |||||||||
History |
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-Structure visualization
-Downloads & links
-EMDB archive
Map data | EMDB map data format | |||
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Header (meta data) | EMDB header | |||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41785 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41785 | HTTPS FTP |
-Validation report
Summary document | emd_41785_validation.pdf.gz | 821.2 KB | Display | EMDB validaton report |
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Full document | emd_41785_full_validation.pdf.gz | 820.8 KB | Display | |
Data in XML | emd_41785_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | emd_41785_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41785 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41785 | HTTPS FTP |
-Related structure data
Related structure data | 8u0uMC 41790 41865 8u0jC 8u0wC 8u3kC 9bqvC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41785.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8332 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : DdmD
Entire | Name: DdmD |
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Components |
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-Supramolecule #1: DdmD
Supramolecule | Name: DdmD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Helicase/UvrB N-terminal domain-containing protein
Supramolecule | Name: Helicase/UvrB N-terminal domain-containing protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: Helicase/UvrB N-terminal domain-containing protein
Macromolecule | Name: Helicase/UvrB N-terminal domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 136.145297 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MNVSIEEFTH FDFQLVPEPS PLDLVITESL KNHIEVNGVK SGALLPLPFQ TGIGKTYTAL NFLLQQMLEQ VRSELKEENT GKKSKRLLY YVTDSVDNVV SAKADLLKLI EKQTVKGEPR FTLEQQEYLK AQIVHLPNQS EQLLQCSDAV LNDVLIGFNL N AERDVQAE ...String: MNVSIEEFTH FDFQLVPEPS PLDLVITESL KNHIEVNGVK SGALLPLPFQ TGIGKTYTAL NFLLQQMLEQ VRSELKEENT GKKSKRLLY YVTDSVDNVV SAKADLLKLI EKQTVKGEPR FTLEQQEYLK AQIVHLPNQS EQLLQCSDAV LNDVLIGFNL N AERDVQAE WSAISGLRRH ASNPEVKISL NRQAGYFYRN LIDRLQKKQK GADRVLLSGS LLASVETLLP GEKIRNGSAH VA FLTTSKF LKGFHNTRSR YSPLRDLSGA VLIIDEIDKQ NQVILSELCK QQAQDLIWAI RTLRANFRDH QLESSPRYDK IED LFEPLR ERLEEFGTNW NLAFAFNTEG ANLNERPVRL FSDRSFTHVS SATHKLSLKS DFLRRKNLIF SDEKVEGSLI EKHG LLTRF VNEADVIYQW FLGTMRKAVF QYWENVRGLE IEVRENRSLE GTFQEAVQSL LTHFNLQEFE SAVYESFDTR GLRQS AGGK ANKLSSSKSY HHTGLKLVEV AHNQGTRDTV NCKASFLNTS PSGVLADMVD AGAVILGISA TARADTVIHN FDFKYL NER LGNKLLSLSR EQKQRVNNYY HSRRNYKDNG VVLTVKYLNS RDAFLDALLE EYKPEARSSH FILNHYLGIA ESEQAFV RS WLSKLLASIK AFISSPDNRY MLSLLNRTLD TTRQNINDFI QFCCDKWAKE FNVKTKTFFG VNADWMRLVG YDEISKHL N TELGKVVVFS TYASMGAGKN PDYAVNLALE GESLISVADV TYSTQLRSDI DSIYLEKPTQ LLLSDDYSHT ANQLCQFHQ ILSLQENGEL SPKSAENWCR QQLMGMSRER SLQQYHQTSD YQSAVRKYIE QAVGRAGRTS LKRKQILLFV DSGLKEILAE ESRDPSLFS HEYVALVNKA KSAGKSIVED RAVRRLFNLA QRNNKDGMLS IKALVHRLHN QPASKSDIQE WQDIRTQLLR Y PTVAFQPE RFNRLYLQSM TKGYYRYQGN LDGDPNSFEF FDRVPYGDMV SEEDCSLATL VQNQYVRPWF ERKGFACSWQ KE ANVMTPI MFTNIYKGAL GEQAVEAVLT AFDFTFEEVP NSIYERFDNR VIFAGIEQPI WLDSKYWKHE GNESSEGYSS KIA LVEEEF GPSKFIYVNA LGDTSKPIRY LNSCFVETSP QLAKVIEIPA LIDDSNADTN RTAVQELIKW LHHS UniProtKB: Helicase/UvrB N-terminal domain-containing protein |
-Macromolecule #2: DNA (5'-D(P*TP*TP*AP*TP*TP*TP*TP*TP*TP*TP*T)-3')
Macromolecule | Name: DNA (5'-D(P*TP*TP*AP*TP*TP*TP*TP*TP*TP*TP*T)-3') / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 3.310177 KDa |
Sequence | String: (DT)(DT)(DA)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) |
-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 (6k x 4k) / Average electron dose: 80.0 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: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 299440 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |