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- EMDB-44516: Structure of V.cholera DdmDE (2D:1E) in complex with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-44516
TitleStructure of V.cholera DdmDE (2D:1E) in complex with DNA
Map dataStructure of V.cholera DdmDE (2D:1E) in complex with DNA
Sample
  • Complex: DdmD dimer bind DdmE in complex with DNA
    • DNA: guide DNA
    • DNA: complementary target DNA
    • DNA: non-complementary target DNA (long)
    • DNA: non-complementary target DNA (short)
    • Protein or peptide: DdmE
    • Protein or peptide: Helicase/UvrB N-terminal domain-containing protein
  • Ligand: MAGNESIUM ION
KeywordsDNA defense modules (Ddm) / DdmDE / anti-plasmid / bacterial immune system / IMMUNE SYSTEM-DNA complex
Function / homologyUncharacterized protein / Helicase/UvrB N-terminal domain-containing protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 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) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44516.png

Downloads & links

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Map

FileDownload / File: emd_44516.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of V.cholera DdmDE (2D:1E) in complex with DNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 256 pix.
= 284.16 Å		1.11 Å/pix.
x 256 pix.
= 284.16 Å		1.11 Å/pix.
x 256 pix.
= 284.16 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: 0.045
Minimum - Maximum-0.030130103 - 2.1678445
Average (Standard dev.)0.0022171068 (±0.03372705)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 284.16 Å
α=β=γ: 90.0 °

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Supplemental data

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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
    • DNA: guide DNA
    • DNA: complementary target DNA
    • DNA: non-complementary target DNA (long)
    • DNA: non-complementary target DNA (short)
    • Protein or peptide: DdmE
    • Protein or peptide: Helicase/UvrB N-terminal domain-containing protein
  • Ligand: MAGNESIUM ION

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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-#6
Source (natural)Organism: Vibrio cholerae (bacteria)

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Macromolecule #1: guide DNA

MacromoleculeName: guide DNA / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 3.767465 KDa
SequenceString:
(DA)(DG)(DG)(DT)(DG)(DA)(DG)(DG)(DA)(DG) (DT)(DC)

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Macromolecule #2: complementary target DNA

MacromoleculeName: complementary target DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 7.594898 KDa
SequenceString:
(DA)(DT)(DG)(DG)(DA)(DC)(DT)(DC)(DC)(DT) (DC)(DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DG) (DT)(DT)(DC)(DA)(DC)

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Macromolecule #3: non-complementary target DNA (long)

MacromoleculeName: non-complementary target DNA (long) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 8.093215 KDa
SequenceString:
(DG)(DT)(DG)(DA)(DA)(DC)(DC)(DT)(DG)(DC) (DA)(DG)(DG)(DT)(DG)(DA)(DG)(DG)(DA)(DG) (DT)(DC)(DC)(DA)(DT)(DG)

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Macromolecule #4: non-complementary target DNA (short)

MacromoleculeName: non-complementary target DNA (short) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 3.702428 KDa
SequenceString:
(DT)(DG)(DA)(DG)(DG)(DA)(DG)(DT)(DC)(DC) (DA)(DT)

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Macromolecule #5: DdmE

MacromoleculeName: DdmE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 79.195891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVTPQLEPSS QGPLSTLIEQ ISIDTDWVDR SFAIYCVSYK GIDFSERPKR LVTLASETYK SGSVYCLVKG ANKEACYWVL LPKDSKLDL KDTSLAIKPS SAAELPTWQL ARLLIKAIPK VLSGTMPEIK RFESEGLYYL VKSKKLPKDH SGYELTTVEI D LAPCAALG ...String:
MVTPQLEPSS QGPLSTLIEQ ISIDTDWVDR SFAIYCVSYK GIDFSERPKR LVTLASETYK SGSVYCLVKG ANKEACYWVL LPKDSKLDL KDTSLAIKPS SAAELPTWQL ARLLIKAIPK VLSGTMPEIK RFESEGLYYL VKSKKLPKDH SGYELTTVEI D LAPCAALG FKQTLSMGTK TFSPLSWFTL ENGEVQKKAR FATRYQLDDV GKLVSKSIKG DYIKKPLYSN AKNRIQAIDI TK ESYSGFQ LSKVGILEQF MQDLKQAYGD SVSVKLQRIP GEKHRFVSDT IVKNHYVGLF DALKEHRLVI CDLTENQDTD AAL TLLHGI EHLDINAEIA EVPIRGALNI LIVGNKDTYK SDEEDPYQVY RKKYQDTVFQ SCYPERLWNR QGQPNRHVVE VLLK ELLIK LEVHTRKHLI EYPSGPERCV YYMPQRPKDE SSEVRDEPWP VYASKLVGDE WQYTQATQEE LEDIELDLGN DKRHV FHGF ERSPVIYWPE TGDYAIFIDT GIQMLPEFEA VAERLRELKE GRSQDVPIAL LAQFIEENPE SKVINKLRAI LSEWDD VAP LPFDEFSTIA YKSSDEKQFY DWLREQGFFL KTSIRGQSEG FFNASLGFFY NREQGMYFAG GKGSPQSKIE TFSHLYL IK HSFDALPEEV ENLFDVYHLR HRLPTVTPYP FKHLREYVEM QRFRS

UniProtKB: Uncharacterized protein

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Macromolecule #6: Helicase/UvrB N-terminal domain-containing protein

MacromoleculeName: Helicase/UvrB N-terminal domain-containing protein / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 136.155328 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNVSIEEFTH FDFQLVPEPS PLDLVITEPL KNHIEVNGVK SGALLPLPFQ TGIGKTYTAL NFLLQQMLEQ VRSELKEENT GKKSKRLLY YVTDSVDNVV SAKADLLKLI EKQTVKGEPR FTLEQQEYLK AQIVHLPNQS EQLLQCSDAV LNDVLIGFNL N AERDVQAE ...String:
MNVSIEEFTH FDFQLVPEPS PLDLVITEPL 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

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 3.28 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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