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- PDB-9c6q: Structure of V. cholerae monomeric DdmD bound with ssDNA -

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Basic information

Entry
Database: PDB / ID: 9c6q
TitleStructure of V. cholerae monomeric DdmD bound with ssDNA
Components
  • Helicase/UvrB N-terminal domain-containing protein
  • ssDNA
KeywordsIMMUNE SYSTEM/DNA / DNA defense modules(Ddm) / DdmDE / Vibrio Cholerae / bacteria / anti-plasmid / IMMUNE SYSTEM-DNA complex
Function / homologyDNA / DNA (> 10) / Helicase/UvrB N-terminal domain-containing protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsShen, Z.F. / Yang, X.Y. / Fu, T.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2024
Title: DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.
Authors: Xiao-Yuan Yang / Zhangfei Shen / Chen Wang / Kotaro Nakanishi / Tian-Min Fu /
Abstract: Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have ...Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgos) and the DNA defense module DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.
History
DepositionJun 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Oct 2, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ssDNA
C: Helicase/UvrB N-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)139,7532
Polymers139,7532
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: DNA chain ssDNA


Mass: 3597.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)
#2: Protein Helicase/UvrB N-terminal domain-containing protein / DdmD


Mass: 136155.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VPI2_0019c / Production host: Escherichia coli (E. coli) / References: UniProt: B9TSM3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Monomeric complex of V. cholerae DdmD bound with ssDNA
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Vibrio cholerae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.21_5207: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 568349 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210061
ELECTRON MICROSCOPYf_angle_d0.54813646
ELECTRON MICROSCOPYf_dihedral_angle_d9.0651433
ELECTRON MICROSCOPYf_chiral_restr0.0391502
ELECTRON MICROSCOPYf_plane_restr0.0031735

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