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- PDB-9ixm: Cryo-EM structure of Lactobacillus casei DdmDE bound with DNA -

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Basic information

Entry
Database: PDB / ID: 9ixm
TitleCryo-EM structure of Lactobacillus casei DdmDE bound with DNA
Components
  • (DNA (30-MER)) x 2
  • DNA (5'-D(P*TP*GP*AP*CP*GP*GP*CP*TP*CP*TP*AP*AP*TP*CP*T)-3')
  • DdmD
  • DdmE
KeywordsDNA BINDING PROTEIN/DNA / Ago / Helicase / Nuclease / DNA BINDING PROTEIN-DNA complex
Function / homologyDNA / DNA (> 10) / Uncharacterized protein
Function and homology information
Biological speciesLacticaseibacillus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 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 29, 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: 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 16, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 16, 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
B: DdmE
C: DdmD
E: DNA (30-MER)
D: DNA (5'-D(P*TP*GP*AP*CP*GP*GP*CP*TP*CP*TP*AP*AP*TP*CP*T)-3')
F: DNA (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,9797
Polymers380,9556
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 3 molecules ACB

#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: Protein DdmE


Mass: 83294.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lacticaseibacillus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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DNA chain , 3 types, 3 molecules EDF

#3: DNA chain DNA (30-MER)


Mass: 9199.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lacticaseibacillus (bacteria)
#4: DNA chain DNA (5'-D(P*TP*GP*AP*CP*GP*GP*CP*TP*CP*TP*AP*AP*TP*CP*T)-3')


Mass: 4559.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lacticaseibacillus (bacteria)
#5: DNA chain DNA (30-MER)


Mass: 9311.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lacticaseibacillus (bacteria)

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

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 DdmDE bound with DNA / Type: COMPLEX / Entity ID: #1-#5 / 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: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94045 / Symmetry type: POINT
RefinementHighest resolution: 3.26 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00321570
ELECTRON MICROSCOPYf_angle_d0.59629445
ELECTRON MICROSCOPYf_dihedral_angle_d17.8193389
ELECTRON MICROSCOPYf_chiral_restr0.0383231
ELECTRON MICROSCOPYf_plane_restr0.0043513

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