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- PDB-8x6x: Structure of the multidrug efflux pump EfpA from M. tuberculosis ... -

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Basic information

Entry
Database: PDB / ID: 8x6x
TitleStructure of the multidrug efflux pump EfpA from M. tuberculosis complexed with lipids
ComponentsUncharacterized MFS-type transporter EfpA
KeywordsMEMBRANE PROTEIN / drug resistance MFS EfpA efflux pump
Function / homology
Function and homology information


transmembrane transporter activity / membrane / plasma membrane
Similarity search - Function
Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
: / : / Uncharacterized MFS-type transporter EfpA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsGao, F. / Zhang, X. / Li, D. / Ma, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)82272379 China
Other government2019A1515110675
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structure and function of EfpA as a lipid transporter and its inhibition by BRD-8000.3.
Authors: Delin Li / Xiaokang Zhang / Yuanhang Yao / Xue Sun / Junqing Sun / Xiaomin Ma / Kai Yuan / Guijie Bai / Xuefei Pang / Rongmao Hua / Tianling Guo / Yuqian Mi / Lingzhi Wu / Jie Zhang / Yan Wu ...Authors: Delin Li / Xiaokang Zhang / Yuanhang Yao / Xue Sun / Junqing Sun / Xiaomin Ma / Kai Yuan / Guijie Bai / Xuefei Pang / Rongmao Hua / Tianling Guo / Yuqian Mi / Lingzhi Wu / Jie Zhang / Yan Wu / Yingxia Liu / Peiyi Wang / Catherine C L Wong / Xiao-Wei Chen / Haixia Xiao / George Fu Gao / Feng Gao /
Abstract: EfpA, the first major facilitator superfamily (MFS) protein identified in (Mtb), is an essential efflux pump implicated in resistance to multiple drugs. EfpA-inhibitors have been developed to kill ...EfpA, the first major facilitator superfamily (MFS) protein identified in (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.
History
DepositionNov 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2025Group: Data collection / Database references
Category: chem_comp_bond / citation ...chem_comp_bond / citation / citation_author / em_admin
Item: _chem_comp_bond.pdbx_stereo_config / _citation.country ..._chem_comp_bond.pdbx_stereo_config / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized MFS-type transporter EfpA
B: Uncharacterized MFS-type transporter EfpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3205
Polymers119,3432
Non-polymers1,9773
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Uncharacterized MFS-type transporter EfpA


Mass: 59671.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: efpA / Production host: Schizosaccharomyces pombe (fission yeast) / References: UniProt: P9WJY5
#2: Chemical ChemComp-Y86 / [(2~{R})-1-[(9~{Z},12~{Z},15~{E})-octadeca-9,12,15-trienoyl]oxy-3-phosphonooxy-propan-2-yl] nonadecanoate


Mass: 712.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H73O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-Y8F / [(2~{S})-1-dodecanoyloxy-3-phosphonooxy-propan-2-yl] tridecanoate


Mass: 550.705 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H55O8P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: EfpA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Source (recombinant)Organism: Schizosaccharomyces pombe (fission yeast)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227843 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 67.32 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00337154
ELECTRON MICROSCOPYf_angle_d0.52459717
ELECTRON MICROSCOPYf_chiral_restr0.03741188
ELECTRON MICROSCOPYf_plane_restr0.00421190
ELECTRON MICROSCOPYf_dihedral_angle_d5.40571115

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