+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41781 | |||||||||
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Title | DdmE in complex with guide and target DNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DdmE / Argonaute / pAgo / IMMUNE SYSTEM / IMMUNE SYSTEM-DNA complex | |||||||||
Function / homology | Uncharacterized protein Function and homology information | |||||||||
Biological species | Streptococcus pyogenes (bacteria) / Vibrio cholerae (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41781.map.gz | 116 MB | EMDB map data format | |
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Header (meta data) | emd-41781-v30.xml emd-41781.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_41781.png | 73.1 KB | ||
Filedesc metadata | emd-41781.cif.gz | 6 KB | ||
Others | emd_41781_half_map_1.map.gz emd_41781_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41781 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41781 | HTTPS FTP |
-Validation report
Summary document | emd_41781_validation.pdf.gz | 929.4 KB | Display | EMDB validaton report |
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Full document | emd_41781_full_validation.pdf.gz | 929 KB | Display | |
Data in XML | emd_41781_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | emd_41781_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41781 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41781 | HTTPS FTP |
-Related structure data
Related structure data | 8u0jMC 8u0uC 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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-Map
File | Download / File: emd_41781.map.gz / Format: CCP4 / Size: 125 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
-Half map: #2
File | emd_41781_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41781_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : DdmE
Entire | Name: DdmE |
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Components |
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-Supramolecule #1: DdmE
Supramolecule | Name: DdmE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Streptococcus pyogenes (bacteria) |
Molecular weight | Theoretical: 211.54 KDa |
-Macromolecule #1: DdmE
Macromolecule | Name: DdmE / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 78.125672 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QGPLSTLIEQ ISIDTDWVDR SFAIYCVSYK GIDFSERPKR LVTLASETYK SGSVYCLVKG ANKEACYWVL LPKDSKLDLK DTSLAIKPS SAAELPTWQL ARLLIKAIPK VLSGTMPEIK RFESEGLYYL VKSKKLPKDH SGYELTTVEI DLAPCAALGF K QTLSMGTK ...String: QGPLSTLIEQ ISIDTDWVDR SFAIYCVSYK GIDFSERPKR LVTLASETYK SGSVYCLVKG ANKEACYWVL LPKDSKLDLK DTSLAIKPS SAAELPTWQL ARLLIKAIPK VLSGTMPEIK RFESEGLYYL VKSKKLPKDH SGYELTTVEI DLAPCAALGF K QTLSMGTK TFSPLSWFTL ENGEVQKKAR FATRYQLDDV GKLVSKSIKG DYIKKPLYSN AKNRIQAIDI TKESYSGFQL SK VGILEQF MQDLKQAYGD SVSVKLQRIP GEKHRFVSDT IVKNHYVGLF DALKEHRLVI CDLTENQDTD AALTLLHGIE HLD INAEIA EVPIRGALNI LIVGNKDTYK SDEEDPYQVY RKKYQDTVFQ SCYPERLWNR QGQPNRHVVE VLLKELLIKL EVHT RKHLI EYPSGPERCV YYMPQRPKDE SSEVRDEPWP VYASKLVGDE WQYTQATQEE LEDIELDLGN DKRHVFHGFE RSPVI YWPE TGDYAIFIDT GIQMLPEFEA VAERLRELKE GRSQDVPIAL LAQFIEENPE SKVINKLRAI LSEWDDVAPL PFDEFS TIA YKSSDEKQFY DWLREQGFFL KTSIRGQSEG FFNASLGFFY NREQGMYFAG GKGSPQSKIE TFSHLYLIKH SFDALPE EV ENLFDVYHLR HRLPTVTPYP FKHLREYVEM QRFRS UniProtKB: Uncharacterized protein |
-Macromolecule #2: DNA (5'-D(P*GP*TP*TP*AP*GP*AP*CP*TP*TP*TP*AP*AP*GP*T)-3')
Macromolecule | Name: DNA (5'-D(P*GP*TP*TP*AP*GP*AP*CP*TP*TP*TP*AP*AP*GP*T)-3') type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 4.309826 KDa |
Sequence | String: (DG)(DT)(DT)(DA)(DG)(DA)(DC)(DT)(DT)(DT) (DA)(DA)(DG)(DT) |
-Macromolecule #3: DNA (5'-D(P*AP*CP*TP*TP*AP*AP*AP*GP*TP*CP*TP*AP*AP*CP*CP*TP*AP*TP...
Macromolecule | Name: DNA (5'-D(P*AP*CP*TP*TP*AP*AP*AP*GP*TP*CP*TP*AP*AP*CP*CP*TP*AP*TP*AP*GP*GP*AP*T)-3') type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 7.047598 KDa |
Sequence | String: (DA)(DC)(DT)(DT)(DA)(DA)(DA)(DG)(DT)(DC) (DT)(DA)(DA)(DC)(DC)(DT)(DA)(DT)(DA)(DG) (DG)(DA)(DT) |
-Macromolecule #4: DNA (5'-D(P*AP*TP*CP*CP*TP*AP*TP*AP*GP*GP*A)-3')
Macromolecule | Name: DNA (5'-D(P*AP*TP*CP*CP*TP*AP*TP*AP*GP*GP*A)-3') / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 3.357223 KDa |
Sequence | String: (DA)(DT)(DC)(DC)(DT)(DA)(DT)(DA)(DG)(DG) (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 |
-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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 594426 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |