+Open data
-Basic information
Entry | Database: PDB / ID: 8u3k | |||||||||
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Title | DdmDE handover complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM/DNA / DdmE / DdmD / pAgo / helicase / nuclease / IMMUNE SYSTEM / IMMUNE SYSTEM-DNA complex | |||||||||
Function / homology | DNA / DNA (> 10) / Uncharacterized protein / Helicase/UvrB N-terminal domain-containing protein Function and homology information | |||||||||
Biological species | Vibrio cholerae (bacteria) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Bravo, J.P.K. | |||||||||
Funding support | United States, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u3k.cif.gz | 561.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u3k.ent.gz | 446.6 KB | Display | PDB format |
PDBx/mmJSON format | 8u3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u3k_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8u3k_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8u3k_validation.xml.gz | 86.9 KB | Display | |
Data in CIF | 8u3k_validation.cif.gz | 132.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/8u3k ftp://data.pdbj.org/pub/pdb/validation_reports/u3/8u3k | HTTPS FTP |
-Related structure data
Related structure data | 41865MC 8u0jC 8u0uC 8u0wC 9bqvC 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 , 2 types, 3 molecules AFE
#1: Protein | Mass: 140011.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ERS013206_03454 / Production host: Escherichia coli (E. coli) / References: UniProt: B9TSM3 #4: Protein | | Mass: 79195.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ERS013165_02654 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H6MQD2 |
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-DNA chain , 3 types, 3 molecules CDG
#2: DNA chain | Mass: 8777.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 4657.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: DNA chain | Mass: 3301.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 1 types, 1 molecules
#6: Chemical | ChemComp-MG / |
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-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: DdmD apo dimer / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: Vibrio cholerae (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
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
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1497134 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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