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- EMDB-44515: Constituent EM map for the consensus map of DdmDE complex -

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Basic information

Entry
Database: EMDB / ID: EMD-44515
TitleConstituent EM map for the consensus map of DdmDE complex
Map data
Sample
  • Complex: DdmD dimer bind DdmE in complex with DNA
    • Other: DdmE incomplex with DNA
KeywordsDNA defense modules (Ddm) / DdmDE / Vibrio cholera / anti-plasmid / bacterial immune system / IMMUNE SYSTEM
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsShen ZF / Yang XY / Fu TM
Funding support1 items
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
DepositionApr 19, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44515.png

Downloads & links

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Map

FileDownload / File: emd_44515.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 360 pix.
= 399.6 Å		1.11 Å/pix.
x 360 pix.
= 399.6 Å		1.11 Å/pix.
x 360 pix.
= 399.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.8371409 - 2.6303132
Average (Standard dev.)0.000000813412 (±0.041594617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 399.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44515_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44515_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DdmD dimer bind DdmE in complex with DNA

EntireName: DdmD dimer bind DdmE in complex with DNA
Components
  • Complex: DdmD dimer bind DdmE in complex with DNA
    • Other: DdmE incomplex with DNA

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Supramolecule #1: DdmD dimer bind DdmE in complex with DNA

SupramoleculeName: DdmD dimer bind DdmE in complex with DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Vibrio cholerae (bacteria)

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Macromolecule #1: DdmE incomplex with DNA

MacromoleculeName: DdmE incomplex with DNA / type: other / ID: 1 / Classification: other
SequenceString: MVTPQLEPSS QGPLSTLIEQ ISIDTDWVDR SFAIYCVSYK GIDF SERPK RLVTLASETY KSGSVYCLVK GANKEACYWV LLPKDSKLDL KDTSLAIKPS SAA ELPTWQ LARLLIKAIP KVLSGTMPEI KRFESEGLYY LVKSKKLPKD HSGYELTTVE ID LAPCAAL ...String:
MVTPQLEPSS QGPLSTLIEQ ISIDTDWVDR SFAIYCVSYK GIDF SERPK RLVTLASETY KSGSVYCLVK GANKEACYWV LLPKDSKLDL KDTSLAIKPS SAA ELPTWQ LARLLIKAIP KVLSGTMPEI KRFESEGLYY LVKSKKLPKD HSGYELTTVE ID LAPCAAL GFKQTLSMGT KTFSPLSWFT LENGEVQKKA RFATRYQLDD VGKLVSKSIK G DYIKKPLY SNAKNRIQAI DITKESYSGF QLSKVGILEQ FMQDLKQAYG DSVSVKLQRI PGEKHRFVS DTIVKNHYVG LFDALKEHRL VICDLTENQD TDAALTLLHG IEHLDINAE IAEVPIRGAL NILIVGNKDT YKSDEEDPYQ VYRKKYQDTV FQSCYPERLW NRQGQPNR H VVEVLLKELL IKLEVHTRKH LIEYPSGPER CVYYMPQRPK DESSEVRDEP WPVYASK LV GDEWQYTQAT QEELEDIELD LGNDKRHVFH GFERSPVIYW PETGDYAIFI DTGIQM LPE FEAVAERLRE LKEGRSQDVP IALLAQFIEE NPESKVINKL RAILSEWDDV APLPF DEFS TIAYKSSDEK QFYDWLREQG FFLKTSIRGQ SEGFFNASLG FFYNREQGMY FAGG KGSPQ SKIETFSHLY LIKHSFDALP EEVENLFDVY HLRHRLPTVT PYPFKHLREY VEM QRFRS

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142963
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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