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- PDB-8qzl: Single particle cryo-EM co-structure of Klebsiella pneumoniae Acr... -

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Basic information

Entry
Database: PDB / ID: 8qzl
TitleSingle particle cryo-EM co-structure of Klebsiella pneumoniae AcrB with the BDM91288 efflux pump inhibitor at 3.42 Angstrom resolution
ComponentsEfflux pump membrane transporter
KeywordsTRANSPORT PROTEIN / Efflux Pump Inhibitor / Transmembrane Binding / Antibiotic Resistance
Function / homology3-chloranyl-2,6-di(piperazin-4-ium-1-yl)quinoline / :
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsBoernsen, C. / Mueller, R.T. / Pos, K.M. / Frangakis, A.S.
Funding support Germany, France, 2items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchBMBF- 16GW0236K Germany
Agence Nationale de la Recherche (ANR)ANR-19-AMRB-0007 France
CitationJournal: To be published
Title: Single particle cryo-EM co-structure of Klebsiella pneumoniae AcrB with the BDM91288 efflux pump inhibitor at 3.42 Angstrom resolution
Authors: Boernsen, C. / Mueller, R.T.
History
DepositionOct 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Efflux pump membrane transporter
B: Efflux pump membrane transporter
C: Efflux pump membrane transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,1385
Polymers343,4703
Non-polymers6682
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 Efflux pump membrane transporter


Mass: 114489.945 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940 (bacteria)
Strain: FDAARGOS_775 / Gene: UUU_08720 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C43(De3)deltaacrB / References: UniProt: J2LW81
#2: Chemical ChemComp-WQW / 3-chloranyl-2,6-di(piperazin-4-ium-1-yl)quinoline


Mass: 333.859 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H24ClN5 / 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: Trimeric Klebsiella pneumoniae AcrB with BDM91288 efflux pump inhibitor
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Klebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940 (bacteria)
Strain: FDAARGOS_775
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: C43(DE3)deltaacrAB
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
2150 mMsodium chlorideNaCl1
30.02 %DDM1
SpecimenConc.: 4.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated magnification: 130000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8487
EM imaging opticsEnergyfilter name: GIF Quantum SE / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
4cryoSPARC4CTF correction
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 380181
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109174 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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