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- EMDB-60964: Cryo-EM structure of Lactobacillus casei DdmD dimer bound with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-60964
TitleCryo-EM structure of Lactobacillus casei DdmD dimer bound with DNA
Map data
Sample
  • Complex: Lactobacillus casei DdmD bound with DNA substrate
    • Protein or peptide: DdmD
    • DNA: DNA (5'-D(P*TP*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')
    • DNA: DNA (5'-D(P*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')
    • DNA: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsAgo / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA complex
Function / homologyUncharacterized protein
Function and homology information
Biological speciesLacticaseibacillus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsHuang PP / Chen MR / Xiao YB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2024
Title: The mechanism of bacterial defense system DdmDE from Lactobacillus casei.
Authors: Pingping Huang / Purui Yan / Lijie Guo / Wenying Fei / Zhaoxing Li / Jingxian Liu / Jianping Kong / Yue Yao / Meiling Lu / Yibei Xiao / Meirong Chen /
History
DepositionJul 26, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60964.png

Downloads & links

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Map

FileDownload / File: emd_60964.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 384 pix.
= 357.888 Å		0.93 Å/pix.
x 384 pix.
= 357.888 Å		0.93 Å/pix.
x 384 pix.
= 357.888 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.37636355 - 0.7530811
Average (Standard dev.)0.00030791762 (±0.017146422)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 357.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60964_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60964_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 : Lactobacillus casei DdmD bound with DNA substrate

EntireName: Lactobacillus casei DdmD bound with DNA substrate
Components
  • Complex: Lactobacillus casei DdmD bound with DNA substrate
    • Protein or peptide: DdmD
    • DNA: DNA (5'-D(P*TP*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')
    • DNA: DNA (5'-D(P*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')
    • DNA: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Lactobacillus casei DdmD bound with DNA substrate

SupramoleculeName: Lactobacillus casei DdmD bound with DNA substrate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Lacticaseibacillus (bacteria)

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Macromolecule #1: DdmD

MacromoleculeName: DdmD / type: protein_or_peptide / ID: 1
Details: Sequence reference for Lacticaseibacillus (2759736) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID A0A5R8LS59.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lacticaseibacillus (bacteria)
Molecular weightTheoretical: 137.294719 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MQVSDFSGMI KKLQSQSPEH ALMLLNAPTG TGKSYTIIRA LCRYAIKHEN FRAFFVTDQK KNLKEQDFEV AWREESGAVH KAFSERVAV VRSLEDTVNK LINDWDRQQI PDLYRSSPIF KKSLENLGNA FKSFGMMKEN EFDLKNAWTM LSRAEYQVRR A MITILADK ...String:
MQVSDFSGMI KKLQSQSPEH ALMLLNAPTG TGKSYTIIRA LCRYAIKHEN FRAFFVTDQK KNLKEQDFEV AWREESGAVH KAFSERVAV VRSLEDTVNK LINDWDRQQI PDLYRSSPIF KKSLENLGNA FKSFGMMKEN EFDLKNAWTM LSRAEYQVRR A MITILADK AHVKLKNISE AGASAFKLDS ISKGKIREFV SKQPKADSKW LNETYPTFDL EKKQIIILTT AKFIKSYTPF FE KRSKAFR YSPILKDALV VLDEFDSTKK QILESAIDEA LKIQADLNSL FVDLSKGLNK VNEGQLPAKL GKSFTFRDAF KEI LNDAEQ LTAEFKLDFL YKMEEQGRDS GFVMRVPQTN WVSVGKPWNA YFDEELRQVV LGRQPRNDLN FQRMLPRISV FLKG ATKFI LNRAREYQVS ENQKLSSLDD AMTIEDACFS IYAALGLSKS QAKILFSLGH DFSSPTKVKT TYHAHSGRRF QQRGL SLFQ FTNDPQHDLQ TKINACFFNE TPERYLLNLL SKANVLGLSA TATLPTVLDN YDLGYLREML GPRLLDGVHY LSDTTI KEF DFESRYAKQK IEVKVETGIV DRFFSEILPK NNQKIDNKKI WELDAELAKL VNCIPASEQS RIDKKYFARR YLNLFNS FV IFLTDPSMTS FLGLQSLLPG ADGRMDENYI KETFTTLKDL VGGQDGVNTE LRIVSSRNQE GIQEQLSEAL NLVSQGGK R VYILSAYQTI GIGQNLQHEM NEFEREQAAN IAPKGVSKSD RRQHTIDLAG MYLGEVTHIL SSNLPFRMDA AGLRSIIEQ EYLFDANEIN IKYLNKYLKG LQHQRLERHP EYARSLYVSY SRTIIQALGR MNRSFNKMPL IRLVMPVNVL QMVTDSGIDV EKTSQEYRC LLTAAKDWER DFEKPSAEIA KQNATFNTFR DYRFVLAYLQ TSKSWAQIYH DTRWFYVRHP TVSDKDLKSS Q VFQQRDDE FGLQYLLNEH LDVSYEVKPI NHDNGQFDFS GTGMEVSAEA AGLVAMCRYP GLKEAFESLD IPTKWEPNER IL NPAQFYN YRGLLGEVSG QFIFQNEWSL KLADFGKPEN YELFDFHWEG KVVIDFKNWR DAPDVDTKAE RQKVEAKLAK LQA NTQREW RVIIINILAS NQTRPVMTVD GKILEISGLI DHQGKFLLTP EQKLNVWRFL NGTAVNDSND TIRLQN

UniProtKB: Uncharacterized protein

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Macromolecule #2: DNA (5'-D(P*TP*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')

MacromoleculeName: DNA (5'-D(P*TP*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Lacticaseibacillus (bacteria)
Molecular weightTheoretical: 3.965609 KDa
SequenceString:
(DT)(DA)(DT)(DG)(DA)(DG)(DT)(DA)(DT)(DA) (DT)(DC)(DC)

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Macromolecule #3: DNA (5'-D(P*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')

MacromoleculeName: DNA (5'-D(P*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Lacticaseibacillus (bacteria)
Molecular weightTheoretical: 3.661416 KDa
SequenceString:
(DA)(DT)(DG)(DA)(DG)(DT)(DA)(DT)(DA)(DT) (DC)(DC)

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Macromolecule #4: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') / type: dna / ID: 4 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Lacticaseibacillus (bacteria)
Molecular weightTheoretical: 3.08711 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 122811
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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