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- EMDB-45254: Structure of V. cholerae monomeric DdmD bound with ssDNA -

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Basic information

Entry
Database: EMDB / ID: EMD-45254
TitleStructure of V. cholerae monomeric DdmD bound with ssDNA
Map data
Sample
  • Complex: Monomeric complex of V. cholerae DdmD bound with ssDNA
    • DNA: ssDNA
    • Protein or peptide: Helicase/UvrB N-terminal domain-containing protein
KeywordsDNA defense modules(Ddm) / DdmDE / Vibrio Cholerae / bacteria / anti-plasmid / IMMUNE SYSTEM-DNA complex
Function / homologyHelicase/UvrB N-terminal domain-containing protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsShen ZF / Yang XY / Fu TM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell(Cambridge,Mass.) / Year: 2024
Title: DdmDE eliminates plasmid invasion by DNA-guided DNA targeting
Authors: Shen ZF / Yang XY / Fu TM
History
DepositionJun 8, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45254.png

Downloads & links

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Map

FileDownload / File: emd_45254.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.45 Å/pix.
x 512 pix.
= 230.144 Å		0.45 Å/pix.
x 512 pix.
= 230.144 Å		0.45 Å/pix.
x 512 pix.
= 230.144 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.4495 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0324
Minimum - Maximum-0.17053305 - 0.2640994
Average (Standard dev.)0.00014946866 (±0.0056991642)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 230.144 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_45254_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45254_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_45254_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 : Monomeric complex of V. cholerae DdmD bound with ssDNA

EntireName: Monomeric complex of V. cholerae DdmD bound with ssDNA
Components
  • Complex: Monomeric complex of V. cholerae DdmD bound with ssDNA
    • DNA: ssDNA
    • Protein or peptide: Helicase/UvrB N-terminal domain-containing protein

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Supramolecule #1: Monomeric complex of V. cholerae DdmD bound with ssDNA

SupramoleculeName: Monomeric complex of V. cholerae DdmD bound with ssDNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)

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Macromolecule #1: ssDNA

MacromoleculeName: ssDNA / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 3.597367 KDa
SequenceString:
(DC)(DT)(DA)(DT)(DT)(DA)(DG)(DC)(DC)(DT) (DC)(DA)

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Macromolecule #2: Helicase/UvrB N-terminal domain-containing protein

MacromoleculeName: Helicase/UvrB N-terminal domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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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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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 568349
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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