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- EMDB-39432: The structure of EfpA_BRD-8000.3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39432
TitleThe structure of EfpA_BRD-8000.3 complex
Map data
Sample
  • Complex: EfpA
    • Protein or peptide: Uncharacterized MFS-type transporter EfpA
  • Ligand: (1S,3S)-N-[6-bromo-5-(pyrimidin-2-yl)pyridin-2-yl]-2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropane-1-carboxamide
KeywordsPROTEIN BINDING
Function / homologyMajor facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / transmembrane transporter activity / MFS transporter superfamily / membrane / plasma membrane / Uncharacterized MFS-type transporter EfpA
Function and homology information
Biological speciesMycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsLi DL / Sun JQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82272379 China
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
DepositionMar 12, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39432.png

Downloads & links

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Map

FileDownload / File: emd_39432.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.097
Minimum - Maximum-0.0016906831 - 1.6770781
Average (Standard dev.)0.0009935196 (±0.021489142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39432_half_map_1.map
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Half map: #1

Fileemd_39432_half_map_2.map
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Sample components

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Entire : EfpA

EntireName: EfpA
Components
  • Complex: EfpA
    • Protein or peptide: Uncharacterized MFS-type transporter EfpA
  • Ligand: (1S,3S)-N-[6-bromo-5-(pyrimidin-2-yl)pyridin-2-yl]-2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropane-1-carboxamide

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Supramolecule #1: EfpA

SupramoleculeName: EfpA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)

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Macromolecule #1: Uncharacterized MFS-type transporter EfpA

MacromoleculeName: Uncharacterized MFS-type transporter EfpA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 59.671445 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe (fission yeast)
SequenceString: MTALNDTERA VRNWTAGRPH RPAPMRPPRS EETASERPSR YYPTWLPSRS FIAAVIAIGG MQLLATMDST VAIVALPKIQ NELSLSDAG RSWVITAYVL TFGGLMLLGG RLGDTIGRKR TFIVGVALFT ISSVLCAVAW DEATLVIARL SQGVGSAIAS P TGLALVAT ...String:
MTALNDTERA VRNWTAGRPH RPAPMRPPRS EETASERPSR YYPTWLPSRS FIAAVIAIGG MQLLATMDST VAIVALPKIQ NELSLSDAG RSWVITAYVL TFGGLMLLGG RLGDTIGRKR TFIVGVALFT ISSVLCAVAW DEATLVIARL SQGVGSAIAS P TGLALVAT TFPKGPARNA ATAVFAAMTA IGSVMGLVVG GALTEVSWRW AFLVNVPIGL VMIYLARTAL RETNKERMKL DA TGAILAT LACTAAVFAF SIGPEKGWMS GITIGSGLVA LAAAVAFVIV ERTAENPVVP FHLFRDRNRL VTFSAILLAG GVM FSLTVC IGLYVQDILG YSALRAGVGF IPFVIAMGIG LGVSSQLVSR FSPRVLTIGG GYLLFGAMLY GSFFMHRGVP YFPN LVMPI VVGGIGIGMA VVPLTLSAIA GVGFDQIGPV SAIALMLQSL GGPLVLAVIQ AVITSRTLYL GGTTGPVKFM NDVQL AALD HAYTYGLLWV AGAAIIVGGM ALFIGYTPQQ VAHAQEVKEA IDAGELAAAE NLYFQGLWSH PQFEKGGGSG GGSGGS AWS HPQFEK

UniProtKB: Uncharacterized MFS-type transporter EfpA

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Macromolecule #2: (1S,3S)-N-[6-bromo-5-(pyrimidin-2-yl)pyridin-2-yl]-2,2-dimethyl-3...

MacromoleculeName: (1S,3S)-N-[6-bromo-5-(pyrimidin-2-yl)pyridin-2-yl]-2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropane-1-carboxamide
type: ligand / ID: 2 / Number of copies: 2 / Formula: A1AQR
Molecular weightTheoretical: 401.3 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 180121
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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