8UFD | pdb_00008ufd

Multidrug efflux pump MtEfpA bound with inhibitor BRD8000.3

• PDB DOI: https://doi.org/10.2210/pdb8UFD/pdb
• EM Map EMD-42204: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Mycobacterium tuberculosis
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-10-04 Released: 2024-09-11 
• Deposition Author(s): Wang, S., Liao, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.26 Å
• Aggregation State: 2D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structures of the Mycobacterium tuberculosis efflux pump EfpA reveal the mechanisms of transport and inhibition.

Wang, S., Wang, K., Song, K., Lai, Z.W., Li, P., Li, D., Sun, Y., Mei, Y., Xu, C., Liao, M.

(2024) Nat Commun 15: 7710-7710

• PubMed: 39231991 
• DOI: https://doi.org/10.1038/s41467-024-51948-9
• Primary Citation Related Structures: 
  8UFD, 8UFE, 8WM5


• PubMed Abstract: 
  

  As the first identified multidrug efflux pump in Mycobacterium tuberculosis (Mtb), EfpA is an essential protein and promising drug target. However, the functional and inhibitory mechanisms of EfpA are poorly understood. Here we report cryo-EM structures of EfpA in outward-open conformation, either bound to three endogenous lipids or the inhibitor BRD-8000.3. Three lipids inside EfpA span from the inner leaflet to the outer leaflet of the membrane. BRD-8000.3 occupies one lipid site at the level of inner membrane leaflet, competitively inhibiting lipid binding. EfpA resembles the related lysophospholipid transporter MFSD2A in both overall structure and lipid binding sites and may function as a lipid flippase. Combining AlphaFold-predicted EfpA structure, which is inward-open, we propose a complete conformational transition cycle for EfpA. Together, our results provide a structural and mechanistic foundation to comprehend EfpA function and develop EfpA-targeting anti-TB drugs.

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Organizational Affiliation: 
• Department of Cell Biology, Harvard Medical School, Boston, MA, USA. [e-mail].
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA. [e-mail].
Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
Cryo-EM Core Facility, University of Massachusetts Chan Medical School, Worcester, MA, USA.
mRNA Center of Excellence, Sanofi, Waltham, USA.
Single Particle, LLC, San Diego, CA, USA.
Cryo-electron microscopy center, Southern University of Science and Technology, Shenzhen, China.
Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai, China.
Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China. [e-mail].
Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, 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: 114.98 kDa 
• Atom Count: 7,164 
• Modeled Residue Count: 950 
• Deposited Residue Count: 1,060 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integral membrane efflux protein EFPA	A, B	530	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: efpA
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
PTY (Subject of Investigation/LOI)	C [auth A], D [auth A], F [auth B], G [auth B]	PHOSPHATIDYLETHANOLAMINE C40 H80 N O8 P NJGIRBISCGPRPF-KXQOOQHDSA-N
WJI (Subject of Investigation/LOI)	E [auth A], H [auth B]	(1S,3S)-N-[6-bromo-5-(pyrimidin-2-yl)pyridin-2-yl]-2,2-dimethyl-3-(2-methylpropyl)cyclopropane-1-carboxamide C19 H23 Br N4 O KQDXNUOVSJVMBP-DZGCQCFKSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.26 Å
• Aggregation State: 2D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Wang, S., Liao, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release