9KN3 | pdb_00009kn3

Cryo-EM structure of LptDEM complex from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb9KN3/pdb
• EM Map EMD-62452: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-18 Released: 2025-07-23 
• Deposition Author(s): Tsukazaki, T., Kohga, H., Miyazaki, R.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.27 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of lipopolysaccharide translocon assembly mediated by the small lipoprotein LptM

Miyazaki, R., Kimoto, M., Kohga, H., Tsukazaki, T.

(2025) Cell Rep 44

• DOI: https://doi.org/10.1016/j.celrep.2025.116013

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 113.36 kDa 
• Atom Count: 7,392 
• Modeled Residue Count: 917 
• Deposited Residue Count: 995 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly protein LptD	A	760	Escherichia coli K-12	Mutation(s): 0  Gene Names: lptD, imp, ostA, yabG, b0054, JW0053
UniProt
Find proteins for P31554 (Escherichia coli (strain K12)) Explore P31554  Go to UniProtKB:  P31554

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly lipoprotein LptE	B	175	Escherichia coli K-12	Mutation(s): 0  Gene Names: lptE, rlpB, b0641, JW0636
UniProt
Find proteins for P0ADC1 (Escherichia coli (strain K12)) Explore P0ADC1  Go to UniProtKB:  P0ADC1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized lipoprotein YifL	C	60	Escherichia coli K-12	Mutation(s): 0  Gene Names: yifL, b4558, JW3781
UniProt
Find proteins for P0ADN6 (Escherichia coli (strain K12)) Explore P0ADN6  Go to UniProtKB:  P0ADN6

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.27 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Tsukazaki, T., Kohga, H., Miyazaki, R.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release