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- PDB-8k1n: mycobacterial efflux pump, substrate-bound state -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8k1n
Titlemycobacterial efflux pump, substrate-bound state
Components
  • Multidrug efflux system ATP-binding protein Rv1218c
  • Multidrug efflux system permease protein Rv1217c
KeywordsTRANSPORT PROTEIN / ABC transporter / efflux pump
Function / homology
Function and homology information


Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / response to antibiotic / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Domain of unknown function DUF4162 / Domain of unknown function (DUF4162) / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CARDIOLIPIN / RIFAMPICIN / Multidrug efflux system permease protein Rv1217c / Multidrug efflux system ATP-binding protein Rv1218c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsWang, Y. / Wu, F. / Zhang, L. / Rao, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170703 China
CitationJournal: To Be Published
Title: mycobacterial efflux pump, substrate-bound state
Authors: Wang, Y. / Wu, F. / Zhang, L. / Rao, Z.
History
DepositionJul 11, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Multidrug efflux system permease protein Rv1217c
E: Multidrug efflux system ATP-binding protein Rv1218c
D: Multidrug efflux system ATP-binding protein Rv1218c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,9675
Polymers123,6803
Non-polymers2,2872
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 Multidrug efflux system permease protein Rv1217c


Mass: 56698.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: Rv1217c / Plasmid: PMV261
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: O05318
#2: Protein Multidrug efflux system ATP-binding protein Rv1218c


Mass: 33491.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: Rv1218c / Plasmid: PMV261
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: O86311, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
#3: Chemical ChemComp-RFP / RIFAMPICIN


Mass: 822.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H58N4O12 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY

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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: ternary complex of an ABC transporter Rv1217c-1218c / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.12 MDa / Experimental value: YES
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Plasmid: PMV261
Buffer solutionpH: 7.4 / Details: 150 mM NaCl, 20 mM NaCl, detergent
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: sample was mono disperse
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 16500 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.4 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6284
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2666646
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168188 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT

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