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- EMDB-44651: Mycobacterium tuberculosis efpA parallel dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-44651
TitleMycobacterium tuberculosis efpA parallel dimer
Map dataSharp map after focused refinement in cryosparc.
Sample
  • Complex: efflux protein A
    • Protein or peptide: Uncharacterized MFS-type transporter EfpA
  • Ligand: (2S)-3-{[(R)-[(2R)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-2-{[(2E,9E,13E)-hexadeca-2,9,13-trienoyl]oxy}propyl (4E,9E,11Z,15E)-octadeca-4,9,11,15-tetraenoate
KeywordsTransporter / 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 (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsKhandelwal NK / Gupta M / Stroud RM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM024485 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structure and inhibition mechanisms of Mycobacterium tuberculosis essential transporter efflux protein A.
Authors: Nitesh Kumar Khandelwal / Meghna Gupta / James E Gomez / Sulyman Barkho / Ziqiang Guan / Ashley Y Eng / Tomohiko Kawate / Sree Ganesh Balasubramani / Andrej Sali / Deborah T Hung / Robert M Stroud /
Abstract: A broad chemical genetic screen in Mycobacterium tuberculosis (Mtb) identified compounds (BRD-8000.3 and BRD-9327) that inhibit the essential efflux pump EfpA. To understand the mechanisms of ...A broad chemical genetic screen in Mycobacterium tuberculosis (Mtb) identified compounds (BRD-8000.3 and BRD-9327) that inhibit the essential efflux pump EfpA. To understand the mechanisms of inhibition, we determined the structures of EfpA with these inhibitors bound at 2.7-3.4 Å resolution. Our structures reveal different mechanisms of inhibition by the two inhibitors. BRD-8000.3 binds in a tunnel contacting the lipid bilayer and extending toward the central cavity to displace the fatty acid chain of a lipid molecule bound in the apo structure, suggesting its blocking of an access route for a natural lipidic substrate. Meanwhile, BRD-9327 binds in the outer vestibule without complete blockade of the substrate path to the outside, suggesting its possible inhibition of the movement necessary for alternate access of the transporter. Our results show EfpA as a potential lipid transporter, explain the basis of the synergy of these inhibitors and their potential for combination anti-tuberculosis therapy.
History
DepositionApr 29, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44651.png

Downloads & links

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Map

FileDownload / File: emd_44651.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharp map after focused refinement in cryosparc.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 440 pix.
= 367.4 Å		0.84 Å/pix.
x 440 pix.
= 367.4 Å		0.84 Å/pix.
x 440 pix.
= 367.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.6142696 - 3.1914077
Average (Standard dev.)-0.00022676417 (±0.04572806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 367.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44651_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpned map after focused refinement in cryosparc.

Fileemd_44651_additional_1.map
Annotationunsharpned map after focused refinement in cryosparc.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B from focused refinement in cryosparc.

Fileemd_44651_half_map_1.map
AnnotationHalf map B from focused refinement in cryosparc.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A from focused refinement in cryosparc.

Fileemd_44651_half_map_2.map
AnnotationHalf map A from focused refinement in cryosparc.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : efflux protein A

EntireName: efflux protein A
Components
  • Complex: efflux protein A
    • Protein or peptide: Uncharacterized MFS-type transporter EfpA
  • Ligand: (2S)-3-{[(R)-[(2R)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-2-{[(2E,9E,13E)-hexadeca-2,9,13-trienoyl]oxy}propyl (4E,9E,11Z,15E)-octadeca-4,9,11,15-tetraenoate

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Supramolecule #1: efflux protein A

SupramoleculeName: efflux protein A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Amino acid 1-4 start codon and GSSG 'expression tag', Amnio acid 5- 12 Flag tag, Amnio acid 13-15 SGS 'expression tag', Amino acid 16-21 thrombin site, Amino acid 22-128 BRIL-Tag, Amino acid ...Details: Amino acid 1-4 start codon and GSSG 'expression tag', Amnio acid 5- 12 Flag tag, Amnio acid 13-15 SGS 'expression tag', Amino acid 16-21 thrombin site, Amino acid 22-128 BRIL-Tag, Amino acid 129-610 Mycobacterium tuberculosis EfpA (truncated from 48 N terminal amino acid) with mutation of Proline at position 171 to Arginine, Amino acid 611-612 SS 'expression tag', Amino acid 613-619 TEV site, Amino acid 620-629 10XHis,
Source (natural)Organism: Mycobacterium (bacteria)
Molecular weightTheoretical: 66.53956 KDa

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Macromolecule #1: Uncharacterized MFS-type transporter EfpA

MacromoleculeName: Uncharacterized MFS-type transporter EfpA / type: protein_or_peptide / ID: 1
Details: Its a fusion protein where N terminal 48 residues of EfpA protein have been replaced by BRIL sequence. It contains P171R mutation in EfpA.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 66.602242 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGSSDYKDDD DKSSGLVPRG SMADLEDNWE TLNDNLKVIE KADNAAQVKD ALTKMRAAAL DAQKATPPKL EDKSPDSPEM KDFRHGFDI LVGQIDDALK LANEGKVKEA QAAAEQLKTT RNAYIQKYLR SFIAAVIAIG GMQLLATMDS TVAIVALPKI Q NELSLSDA ...String:
MGSSDYKDDD DKSSGLVPRG SMADLEDNWE TLNDNLKVIE KADNAAQVKD ALTKMRAAAL DAQKATPPKL EDKSPDSPEM KDFRHGFDI LVGQIDDALK LANEGKVKEA QAAAEQLKTT RNAYIQKYLR SFIAAVIAIG GMQLLATMDS TVAIVALPKI Q NELSLSDA GRSWVITAYV LTFGGLMLLG GRLGDTIGRK RTFIVGVALF TISSVLCAVA WDEATLVIAR LSQGVGSAIA SP TGLALVA TTFRKGPARN AATAVFAAMT AIGSVMGLVV GGALTEVSWR WAFLVNVPIG LVMIYLARTA LRETNKERMK LDA TGAILA TLACTAAVFA FSIGPEKGWM SGITIGSGLV ALAAAVAFVI VERTAENPVV PFHLFRDRNR LVTFSAILLA GGVM FSLTV CIGLYVQDIL GYSALRAGVG FIPFVIAMGI GLGVSSQLVS RFSPRVLTIG GGYLLFGAML YGSFFMHRGV PYFPN LVMP IVVGGIGIGM AVVPLTLSAI AGVGFDQIGP VSAIALMLQS LGGPLVLAVI QAVITSRTLY LGGTTGPVKF MNDVQL AAL DHAYTYGLLW VAGAAIIVGG MALFIGYTPQ QVAHAQEVKE AIDAGELSSE NLYFQGHHHH HHHHHH

UniProtKB: Uncharacterized MFS-type transporter EfpA

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Macromolecule #2: (2S)-3-{[(R)-[(2R)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-...

MacromoleculeName: (2S)-3-{[(R)-[(2R)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-2-{[(2E,9E,13E)-hexadeca-2,9,13-trienoyl]oxy}propyl (4E,9E,11Z,15E)-octadeca-4,9,11,15-tetraenoate
type: ligand / ID: 2 / Number of copies: 4 / Formula: A1ATG
Molecular weightTheoretical: 736.912 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

Concentration16.16 mg/mL
BufferpH: 7.5 / Details: 50mM Tris-HCL, 300 mM NaCL, 0.02% GDN,
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 0.033 kPa / Details: 30 second hold 30 second glow
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 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

Particle selectionNumber selected: 10225285
CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 174650
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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