8X6X | pdb_00008x6x

Structure of the multidrug efflux pump EfpA from M. tuberculosis complexed with lipids

• PDB DOI: https://doi.org/10.2210/pdb8X6X/pdb
• EM Map EMD-38093: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Mycobacterium tuberculosis
• Expression System: Schizosaccharomyces pombe
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-11-22 Released: 2024-11-27 
• Deposition Author(s): Gao, F., Zhang, X., Li, D., Ma, X.
• Funding Organization(s): National Science Foundation (NSF, China), Other government

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and function of Mycobacterium tuberculosis EfpA as a lipid transporter and its inhibition by BRD-8000.3.

Li, D., Zhang, X., Yao, Y., Sun, X., Sun, J., Ma, X., Yuan, K., Bai, G., Pang, X., Hua, R., Guo, T., Mi, Y., Wu, L., Zhang, J., Wu, Y., Liu, Y., Wang, P., Wong, C.C.L., Chen, X.W., Xiao, H., Gao, G.F., Gao, F.

(2024) Proc Natl Acad Sci U S A 121: e2412653121-e2412653121

• PubMed: 39441632 
• DOI: https://doi.org/10.1073/pnas.2412653121
• Primary Citation Related Structures: 
  8X6X, 8YNZ


• PubMed Abstract: 
  

  EfpA, the first major facilitator superfamily (MFS) protein identified in Mycobacterium tuberculosis (Mtb), is an essential efflux pump implicated in resistance to multiple drugs. EfpA-inhibitors have been developed to kill drug-tolerant Mtb. However, the biological function of EfpA has not yet been elucidated. Here, we present the cryo-EM structures of EfpA complexed with lipids or the inhibitor BRD-8000.3 at resolutions of 2.9 Å and 3.4 Å, respectively. Unexpectedly, EfpA forms an antiparallel dimer. Functional studies reveal that EfpA is a lipid transporter and BRD-8000.3 inhibits its lipid transport activity. Intriguingly, the mutation V319F, known to confer resistance to BRD-8000.3, alters the expression level and oligomeric state of EfpA. Based on our results and the observation of other antiparallel dimers in the MFS family, we propose an antiparallel-function model of EfpA. Collectively, our work provides structural and functional insights into EfpA's role in lipid transport and drug resistance, which would accelerate the development of antibiotics against this promising drug target.

---

Organizational Affiliation: 
• Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
Shanxi Academy of Advanced Research and Innovation, Taiyuan 030032, China.
Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
College of Future Technology, Peking University, Beijing 100871, China.
First School of Clinical Medicine, Peking University Health Science Center, Peking University, Beijing 100871, China.
Shanxi Agricultural University, Jinzhong, Shanxi 030801, China.
Cryo-EM Center, Southern University of Science and Technology, Shenzhen 518055, China.
Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China.
Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China.
State Key Laboratory of Complex, Severe and Rare Diseases, Clinical Research Institute, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China.
State Key Laboratory of Membrane Biology, Peking University, Center for Life Sciences, Peking University, Beijing 100871, China.
Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 121.32 kDa 
• Atom Count: 7,021 
• Modeled Residue Count: 944 
• Deposited Residue Count: 1,138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized MFS-type transporter EfpA	A, B	569	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: efpA Membrane Entity: Yes
UniProt
Find proteins for P9WJY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJY5  Go to UniProtKB:  P9WJY5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y86 (Subject of Investigation/LOI)	C [auth A], E [auth B]	[(2~{R})-1-[(9~{Z},12~{Z},15~{E})-octadeca-9,12,15-trienoyl]oxy-3-phosphonooxy-propan-2-yl] nonadecanoate C40 H73 O8 P KFUUFNCFVCOTMA-YBEDGUJDSA-N
Y8F (Subject of Investigation/LOI)	D [auth A]	[(2~{S})-1-dodecanoyloxy-3-phosphonooxy-propan-2-yl] tridecanoate C28 H55 O8 P HSXSRFZJKUWGTG-SANMLTNESA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Gao, F., Zhang, X., Li, D., Ma, X.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	82272379
Other government		2019A1515110675

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release
  
• Version 1.1: 2025-12-10
  Changes: Data collection, Database references