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- PDB-9ix4: Cryo-EM structure of Lactobacillus casei DdmD dimer bound with DNA -

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Basic information

Entry
Database: PDB / ID: 9ix4
TitleCryo-EM structure of Lactobacillus casei DdmD dimer bound with DNA
Components
  • DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • DNA (5'-D(P*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')
  • DNA (5'-D(P*TP*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')
  • DdmD
KeywordsDNA BINDING PROTEIN/DNA / Ago / DNA BINDING PROTEIN-DNA complex
Function / homologyADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / Uncharacterized protein
Function and homology information
Biological speciesLacticaseibacillus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsHuang, P.P. / Chen, M.R. / Xiao, Y.B.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.0Jan 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 1, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 1, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 1, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 1, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 1, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DdmD
C: DNA (5'-D(P*TP*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')
B: DdmD
D: DNA (5'-D(P*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')
E: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
F: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,2458
Polymers288,3916
Non-polymers8542
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: Protein DdmD


Mass: 137294.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Lacticaseibacillus (2759736) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID A0A5R8LS59.
Source: (gene. exp.) Lacticaseibacillus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5R8LS59
#2: DNA chain DNA (5'-D(P*TP*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')


Mass: 3965.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lacticaseibacillus (bacteria)
#3: DNA chain DNA (5'-D(P*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')


Mass: 3661.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lacticaseibacillus (bacteria)
#4: DNA chain DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3087.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Lacticaseibacillus (bacteria)
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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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: Lactobacillus casei DdmD bound with DNA substrate / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Lacticaseibacillus (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122811 / Symmetry type: POINT
RefinementHighest resolution: 2.96 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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