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- EMDB-38093: Structure of the multidrug efflux pump EfpA from M. tuberculosis ... -

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Basic information

Entry
Database: EMDB / ID: EMD-38093
TitleStructure of the multidrug efflux pump EfpA from M. tuberculosis complexed with lipids
Map data
Sample
  • Complex: EfpA
    • Protein or peptide: Uncharacterized MFS-type transporter EfpA
  • Ligand: [(2~{R})-1-[(9~{Z},12~{Z},15~{E})-octadeca-9,12,15-trienoyl]oxy-3-phosphonooxy-propan-2-yl] nonadecanoate
  • Ligand: [(2~{S})-1-dodecanoyloxy-3-phosphonooxy-propan-2-yl] tridecanoate
Keywordsdrug resistance MFS EfpA efflux pump / MEMBRANE PROTEIN
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 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsGao F / Zhang X / Li D / Ma X
Funding support China, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)82272379 China
Other government2019A1515110675
CitationJournal: To Be Published
Title: Structure of the multidrug efflux pump EfpA from M. tuberculosis complexed with lipids
Authors: Gao F / Zhang X / Li D / Ma X
History
DepositionNov 22, 2023-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38093.png

Downloads & links

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Map

FileDownload / File: emd_38093.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 342. Å		0.86 Å/pix.
x 400 pix.
= 342. Å		0.86 Å/pix.
x 400 pix.
= 342. Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.136
Minimum - Maximum-0.27334476 - 0.6283242
Average (Standard dev.)-0.00062541437 (±0.012821064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38093_msk_1.map
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Mask #2

Fileemd_38093_msk_2.map
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Half map: #2

Fileemd_38093_half_map_1.map
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Half map: #1

Fileemd_38093_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: [(2~{R})-1-[(9~{Z},12~{Z},15~{E})-octadeca-9,12,15-trienoyl]oxy-3-phosphonooxy-propan-2-yl] nonadecanoate
  • Ligand: [(2~{S})-1-dodecanoyloxy-3-phosphonooxy-propan-2-yl] tridecanoate

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Supramolecule #1: EfpA

SupramoleculeName: EfpA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis (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 (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: [(2~{R})-1-[(9~{Z},12~{Z},15~{E})-octadeca-9,12,15-trienoyl]oxy-3...

MacromoleculeName: [(2~{R})-1-[(9~{Z},12~{Z},15~{E})-octadeca-9,12,15-trienoyl]oxy-3-phosphonooxy-propan-2-yl] nonadecanoate
type: ligand / ID: 2 / Number of copies: 2 / Formula: Y86
Molecular weightTheoretical: 712.977 Da

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Macromolecule #3: [(2~{S})-1-dodecanoyloxy-3-phosphonooxy-propan-2-yl] tridecanoate

MacromoleculeName: [(2~{S})-1-dodecanoyloxy-3-phosphonooxy-propan-2-yl] tridecanoate
type: ligand / ID: 3 / Number of copies: 1 / Formula: Y8F
Molecular weightTheoretical: 550.705 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 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: ab initio 3d by cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 227843
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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