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

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Basic information

Entry
Database: PDB / ID: 9nej
TitleAZD-3 bound EFPA transporter of Mycobacterium tuberculosis
ComponentsUncharacterized MFS-type transporter EfpA
KeywordsMEMBRANE PROTEIN / Transporter
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 H37Rv (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKhandelwal, N.K. / Gupta, M. / Stroud, R.M.
Funding support United States, 1items
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, N.K. / Gupta, M. / Stroud, R.M.
History
DepositionFeb 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)138,35310
Polymers133,2042
Non-polymers5,1488
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Uncharacterized MFS-type transporter EfpA / Efflux protein A


Mass: 66602.242 Da / Num. of mol.: 2 / Mutation: P171R
Source method: isolated from a genetically manipulated source
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
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: efpA, Rv2846c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WJY5
#2: Chemical
ChemComp-A1ATG / (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


Mass: 736.912 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H65O10P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1BXT / (2R)-3-{[(S)-[(2R)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-2-{[(10E)-hexadec-10-enoyl]oxy}propyl (9E,14E)-octadeca-9,14-dienoate


Mass: 744.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H73O10P
#4: Chemical ChemComp-A1BXW / (2P)-2-(2-methoxyphenyl)-N-(3-methoxyphenyl)-1-methyl-1H-pyrrolo[3,2-c]pyridin-4-amine


Mass: 359.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H21N3O2 / 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: Plasma membrane / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: .6 MDa / Experimental value: NO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 7.5 / Details: 50 mM Tris-Cl pH 7.5 300 mM NaCl 0.2% GDN
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris bufferTris-HCl1
2300 mMSodium ChlorideNaCl1
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 10 mg /mL protein with final concentration of 200 uM AZD-3 compound
Specimen supportDetails: 30 Sec glow 30 Sec hold at 15 mA at 0.33 mBar. / Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.18 K
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.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14241

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCv4.2.1particle selection
2SerialEMv4.1image acquisitionbeta software
4cryoSPARCv4.2.1CTF correction
9cryoSPARCv4.2.1initial Euler assignment
10cryoSPARCv4.2.1final Euler assignment
11cryoSPARCv4.2.1classification
12cryoSPARCv4.2.13D reconstruction
13PHENIX1.21_5207-000model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 7213420
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167563 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 102.4 / Protocol: AB INITIO MODEL
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047342
ELECTRON MICROSCOPYf_angle_d0.7229938
ELECTRON MICROSCOPYf_dihedral_angle_d19.211262
ELECTRON MICROSCOPYf_chiral_restr0.0381190
ELECTRON MICROSCOPYf_plane_restr0.0061202

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