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- PDB-9iw3: Cryo-EM structure of Lactobacillus casei DdmE bound with guide an... -

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Basic information

Entry
Database: PDB / ID: 9iw3
TitleCryo-EM structure of Lactobacillus casei DdmE bound with guide and target
Components
  • DNA (25-MER)
  • DNA (5'-D(P*CP*TP*TP*GP*AP*TP*AP*CP*GP*AP*C)-3')
  • DNA (5'-D(P*TP*GP*AP*CP*GP*GP*CP*TP*CP*TP*AP*AP*TP*CP*T)-3')
  • DdmE
KeywordsDNA BINDING PROTEIN/DNA / Ago / DNA BINDING PROTEIN-DNA complex
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesLacticaseibacillus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 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 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: DNA (25-MER)
B: DNA (5'-D(P*TP*GP*AP*CP*GP*GP*CP*TP*CP*TP*AP*AP*TP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*TP*GP*AP*TP*AP*CP*GP*AP*C)-3')
A: DdmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9195
Polymers98,8954
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

#1: DNA chain DNA (25-MER)


Mass: 7706.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lacticaseibacillus (bacteria)
#2: 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)
#3: DNA chain DNA (5'-D(P*CP*TP*TP*GP*AP*TP*AP*CP*GP*AP*C)-3')


Mass: 3333.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lacticaseibacillus (bacteria)
#4: 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)
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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 DdmE bound with guide and target / 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: 2200 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18580 / Symmetry type: POINT

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