9IW3 | pdb_00009iw3

Cryo-EM structure of Lactobacillus casei DdmE bound with guide and target

• PDB DOI: https://doi.org/10.2210/pdb9IW3/pdb
• NAKB: 9IW3
• EM Map EMD-60944: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Lacticaseibacillus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-25 Released: 2025-01-01 
• Deposition Author(s): Huang, P.P., Chen, M.R., Xiao, Y.B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.58 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The mechanism of bacterial defense system DdmDE from Lactobacillus casei.

Huang, P., Yan, P., Guo, L., Fei, W., Li, Z., Liu, J., Kong, J., Yao, Y., Lu, M., Xiao, Y., Chen, M.

(2024) Cell Res 34: 873-876

• PubMed: 39448873 
• DOI: https://doi.org/10.1038/s41422-024-01042-y
• Primary Citation Related Structures: 
  9IW3, 9IX4, 9IXM

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Organizational Affiliation: 
• Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China.
State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China.
Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, China.
Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu, China.
Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China. [e-mail].
State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China. [e-mail].
Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, China. [e-mail].
Engineering Research Center for Anti-infective Drug Discovery, Ministry of Education (ERCADD), Nanjing, Jiangsu, China. [e-mail].
Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China. [e-mail].
State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China. [e-mail].
Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 98.92 kDa 
• Atom Count: 6,879 
• Modeled Residue Count: 763 
• Deposited Residue Count: 766 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DdmE	D [auth A]	715	Lacticaseibacillus	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	A [auth C]	25	Lacticaseibacillus

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*GP*AP*CP*GP*GP*CP*TP*CP*TP*AP*AP*TP*CP*T)-3')	B	15	Lacticaseibacillus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*TP*TP*GP*AP*TP*AP*CP*GP*AP*C)-3')	C [auth D]	11	Lacticaseibacillus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.58 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-01 
Deposition Author(s): Huang, P.P., Chen, M.R., Xiao, Y.B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-01-01
  Type: Initial release