9IX4 | pdb_00009ix4

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

• PDB DOI: https://doi.org/10.2210/pdb9IX4/pdb
• NAKB: 9IX4
• EM Map EMD-60964: EMDB EMDataResource

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


• Deposited: 2024-07-26 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: 2.96 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 289.25 kDa 
• Atom Count: 19,997 
• Modeled Residue Count: 2,393 
• Deposited Residue Count: 2,429 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DdmD	A, C [auth B]	1,192	Lacticaseibacillus	Mutation(s): 0
UniProt
Find proteins for A0A5R8LS59 (Lacticaseibacillus zeae) Explore A0A5R8LS59  Go to UniProtKB:  A0A5R8LS59

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')	B [auth C]	13	Lacticaseibacillus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*TP*GP*AP*GP*TP*AP*TP*AP*TP*CP*C)-3')	D	12	Lacticaseibacillus

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')	E, F	10	Lacticaseibacillus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	G [auth A], H [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.96 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

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
  
• Version 1.1: 2025-07-23
  Changes: Data collection