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- PDB-9bl7: Mycobacterium tuberculosis efpA parallel dimer -

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Basic information

Entry
Database: PDB / ID: 9bl7
TitleMycobacterium tuberculosis efpA parallel dimer
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: 3.22 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)GM024485 United States
CitationJournal: To Be Published
Title: Mycobacterium tuberculosis EFPA parallel dimer
Authors: Khandelwal, N.K. / Gupta, M. / Stroud, R.M.
History
DepositionApr 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Jun 4, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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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)136,1526
Polymers133,2042
Non-polymers2,9484
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: Its a fusion protein where N terminal 48 residues of EfpA protein have been replaced by BRIL sequence. It contains P171R mutation in EfpA.
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: efpA, Rv2846c / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / 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.: 4 / Source method: obtained synthetically / Formula: C40H65O10P
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: efflux protein A / Type: COMPLEX
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,
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.06653956 MDa / Experimental value: NO
Source (natural)Organism: Mycobacterium (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pET28
Buffer solutionpH: 7.5 / Details: 50mM Tris-HCL, 300 mM NaCL, 0.02% GDN,
SpecimenConc.: 16.16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 30 second hold 30 second glow / Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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 / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
8PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 10225285
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174650 / Symmetry type: POINT

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