7MDX

LolCDE nucleotide-free

• PDB DOI: https://doi.org/10.2210/pdb7MDX/pdb
• EM Map EMD-23783: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2021-04-06 Released: 2021-08-11 
• Deposition Author(s): Sharma, S., Liao, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanism of LolCDE as a molecular extruder of bacterial triacylated lipoproteins

Sharma, S., Zhou, R., Wan, L., Feng, S., Song, K., Xu, C., Li, Y., Liao, M.

(2021) Nat Commun 12: 4687

• DOI: https://doi.org/10.1038/s41467-021-24965-1

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 135.64 kDa 
• Atom Count: 9,513 
• Modelled Residue Count: 1,238 
• Deposited Residue Count: 1,238 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein-releasing system transmembrane protein LolC	A	393	Escherichia coli	Mutation(s): 0  Gene Names: lolC, ycfU, b1116, JW5161 Membrane Entity: Yes
UniProt
Find proteins for P0ADC3 (Escherichia coli (strain K12)) Explore P0ADC3  Go to UniProtKB:  P0ADC3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein-releasing system transmembrane protein LolE	B	403	Escherichia coli	Mutation(s): 0  Gene Names: lolE, ycfW, b1118, JW1104 Membrane Entity: Yes
UniProt
Find proteins for P75958 (Escherichia coli (strain K12)) Explore P75958  Go to UniProtKB:  P75958

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein-releasing system ATP-binding protein LolD	C [auth D], D [auth C]	218	Escherichia coli	Mutation(s): 0  Gene Names: lolD, ycfV, b1117, JW5162 EC: 7.6.2 Membrane Entity: Yes
UniProt
Find proteins for P75957 (Escherichia coli (strain K12)) Explore P75957  Go to UniProtKB:  P75957

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Triacyl-lipoprotein	E	6	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZM5 (Subject of Investigation/LOI)	G [auth E]	(2R)-2-(tridecanoyloxy)propyl hexadecanoate C32 H62 O5 ZMBQEERVAJRJTB-SSEXGKCCSA-N
F15 (Subject of Investigation/LOI)	F [auth E]	PENTADECANOIC ACID C15 H30 O2 WQEPLUUGTLDZJY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-11 
Deposition Author(s): Sharma, S., Liao, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2021-08-11
  Type: Initial release
  
• Version 2.0: 2022-02-16
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.0: 2024-04-17
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.1: 2024-10-23
  Changes: Data collection, Structure summary