7MDY | pdb_00007mdy

LolCDE nucleotide-bound

• PDB DOI: https://doi.org/10.2210/pdb7MDY/pdb
• EM Map EMD-23784: 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)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 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: 141.45 kDa 
• Atom Count: 9,733 
• Modeled Residue Count: 1,263 
• Deposited Residue Count: 1,285 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein transporter subunit LolE	A [auth B]	414	Escherichia coli	Mutation(s): 0  Gene Names: lolE Membrane Entity: Yes
UniProt
Find proteins for P75958 (Escherichia coli (strain K12)) Explore P75958  Go to UniProtKB:  P75958

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipo-releasing system transmembrane protein lolC	B [auth A]	399	Escherichia coli	Mutation(s): 0  EC: 3.6.3 Membrane Entity: Yes
UniProt
Find proteins for P0ADC3 (Escherichia coli (strain K12)) Explore P0ADC3  Go to UniProtKB:  P0ADC3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein-releasing system ATP-binding protein LolD	C [auth D], D [auth C]	236	Escherichia coli	Mutation(s): 0  Gene Names: lolD_2, lolD, NCTC10767_05075, NCTC9001_00974 EC: 7.6.2 Membrane Entity: Yes
UniProt
Find proteins for P75957 (Escherichia coli (strain K12)) Explore P75957  Go to UniProtKB:  P75957

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AOV	E [auth D], G [auth C]	ADP ORTHOVANADATE C10 H17 N5 O14 P2 V SWCHWRVRYDCWAN-AZGWGOJFSA-J
MG	F [auth D], H [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 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.

---

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 1.1: 2021-08-18
  Changes: Structure summary
• Version 1.2: 2024-05-29
  Changes: Data collection