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- PDB-9biq: BRD-9327 bound EFPA transporter of Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 9biq
TitleBRD-9327 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
: / : / CHOLESTEROL HEMISUCCINATE / Uncharacterized MFS-type transporter EfpA
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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: BRD-8000.3 bound EFPA transporter of Mycobacterium tuberculosis
Authors: Khandelwal, N.K. / Gupta, M. / Stroud, R.M.
History
DepositionApr 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: 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)139,56112
Polymers133,2042
Non-polymers6,35610
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: Amino acid 1-4 start codon and GSSG linker, Amnio acid 5- 12 Flag tag, Amnio acid 13-15 SGS linker, Amino acid 16-21 thrombin site, Amino acid 22-128 BRIL-Tag, Amino acid 129-610 ...Details: Amino acid 1-4 start codon and GSSG linker, Amnio acid 5- 12 Flag tag, Amnio acid 13-15 SGS linker, 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 linker, Amino acid 613-619 TEV site, Amino acid 620-629 10XHis.
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: efpA, Rv2846c / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P9WJY5
#2: Chemical ChemComp-A1APN / N-(7-benzoyl-2,3-dihydro-1,4-benzodioxin-6-yl)-2-bromobenzamide


Mass: 438.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H16BrNO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-A1H2V / [(2~{R})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] octadecanoate / (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRA N-3,4-DIOL / NEOMYCIN A / NEAMINE / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-glucoside


Mass: 751.023 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H79O10P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50O4 / 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: EfpA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.06653956 MDa / Experimental value: NO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria) / Strain: H37Rv
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Buffer solutionpH: 7.5 / Details: 50mM Tris-HCL, 300 mM NaCL, 0.02% GDN, 0.002 %CHS
Buffer component
IDConc.NameFormulaBuffer-ID
1300 mMSodium chlorideNaCl1
250 mMTrisTris1
SpecimenConc.: 8.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Protein incubated with BRD-9327 200 micro molar final concentration on ice for 15 and used for grid preparation.
Specimen supportDetails: 30 second hold 30 second glow / 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: 281.15 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
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12748

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.2.1particle selection
2SerialEMv4.1 beta softwareimage acquisition
4cryoSPARCv4.2.1CTF correction
11cryoSPARCv4.2.1final Euler assignment
12cryoSPARCv4.2.1classification
13cryoSPARCv4.2.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 6611957
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 181221 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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