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- EMDB-49313: AZD-3 bound EFPA transporter of Mycobacterium tuberculosis -

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Basic information

Entry
Database: EMDB / ID: EMD-49313
TitleAZD-3 bound EFPA transporter of Mycobacterium tuberculosis
Map dataSharpened final map used for model building.
Sample
  • Organelle or cellular component: Plasma membrane
    • 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
  • Ligand: (2R)-3-{[(S)-[(2R)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-2-{[(10E)-hexadec-10-enoyl]oxy}propyl (9E,14E)-octadeca-9,14-dienoate
  • Ligand: (2P)-2-(2-methoxyphenyl)-N-(3-methoxyphenyl)-1-methyl-1H-pyrrolo[3,2-c]pyridin-4-amine
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 tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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)R01GM024485 United States
CitationJournal: To Be Published
Title: AZD-3 bound EFPA transporter of Mycobacterium tuberculosis
Authors: Khandelwal NK / Gupta M / Stroud RM
History
DepositionFeb 19, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49313.png

Downloads & links

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Map

FileDownload / File: emd_49313.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened final map used for model building.
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: 0.4
Minimum - Maximum-2.1428607 - 3.4831486
Average (Standard dev.)-0.00017264337 (±0.058743767)
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_49313_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened EM map.

Fileemd_49313_additional_1.map
AnnotationUnsharpened EM map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A.

Fileemd_49313_half_map_1.map
Annotationhalf map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B.

Fileemd_49313_half_map_2.map
Annotationhalf map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Plasma membrane

EntireName: Plasma membrane
Components
  • Organelle or cellular component: Plasma membrane
    • 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
  • Ligand: (2R)-3-{[(S)-[(2R)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-2-{[(10E)-hexadec-10-enoyl]oxy}propyl (9E,14E)-octadeca-9,14-dienoate
  • Ligand: (2P)-2-(2-methoxyphenyl)-N-(3-methoxyphenyl)-1-methyl-1H-pyrrolo[3,2-c]pyridin-4-amine

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Supramolecule #1: Plasma membrane

SupramoleculeName: Plasma membrane / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 600 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: First 47 amino acid of efpA (uniprot id: P9WJY5) replaced by N- Start codon with linker followed by N-terminal FLAG tag Followed by linker sequence with Thrombin site Followed by BRIL TAG ...Details: First 47 amino acid of efpA (uniprot id: P9WJY5) replaced by N- Start codon with linker followed by N-terminal FLAG tag Followed by linker sequence with Thrombin site Followed by BRIL TAG Followed EFPA sequence with P171R mutation Followed by TEV site Followed by 10X-HIS tag
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 66.602242 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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: 5 / Formula: A1ATG
Molecular weightTheoretical: 736.912 Da

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

MacromoleculeName: (2R)-3-{[(S)-[(2R)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-2-{[(10E)-hexadec-10-enoyl]oxy}propyl (9E,14E)-octadeca-9,14-dienoate
type: ligand / ID: 3 / Number of copies: 1 / Formula: A1BXT
Molecular weightTheoretical: 744.975 Da

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Macromolecule #4: (2P)-2-(2-methoxyphenyl)-N-(3-methoxyphenyl)-1-methyl-1H-pyrrolo[...

MacromoleculeName: (2P)-2-(2-methoxyphenyl)-N-(3-methoxyphenyl)-1-methyl-1H-pyrrolo[3,2-c]pyridin-4-amine
type: ligand / ID: 4 / Number of copies: 2 / Formula: A1BXW
Molecular weightTheoretical: 359.421 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

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTris-HClTris buffer
300.0 mMNaClSodium Chloride

Details: 50 mM Tris-Cl pH 7.5 300 mM NaCl 0.2% GDN
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.033 kPa / Details: 30 Sec glow 30 Sec hold at 15 mA at 0.33 mBar.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.18 K / Instrument: FEI VITROBOT MARK IV
Details: protein complex sample at concentration of 10 mg/mL was applied to cryo-EM grids blotted for 4.5 second followed by plunge-freezing in liquid ethane..
Details10 mg /mL protein with final concentration of 200 uM AZD-3 compound

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 14241 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 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: 7213420
CTF correctionSoftware - Name: cryoSPARC (ver. v4.2.1) / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9bii


Details: EfpA apo model published by us.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.2.1) / Number images used: 167563
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL / Overall B value: 102.4
Output model

PDB-9nej:
AZD-3 bound EFPA transporter of Mycobacterium tuberculosis

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