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- EMDB-50334: Single particle cryo-EM structure of the multidrug efflux pump Oq... -

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Basic information

Entry
Database: EMDB / ID: EMD-50334
TitleSingle particle cryo-EM structure of the multidrug efflux pump OqxB from Klebsiella pneumoniae
Map data
Sample
  • Complex: Trimeric Klebsiella pneumoniae efflux pump membrane transporter OqxB
    • Protein or peptide: Efflux pump membrane transporter
KeywordsDrug efflux / RND transporter / TRANSPORT PROTEIN
Function / homologyHydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / plasma membrane / Efflux pump membrane transporter
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsLazarova M / Frangakis A / Pos KM
Funding support Switzerland, Germany, 4 items
OrganizationGrant numberCountry
Swiss National Science Foundation3100A0_118402 Switzerland
German Research Foundation (DFG)SFB807-P18 Germany
German Research Foundation (DFG)SFB1507-P3 Germany
German Research Foundation (DFG)DFG-EXC115 Germany
CitationJournal: To Be Published
Title: Single particle cryo-EM structure of the multidrug efflux pump OqxB from Klebsiella pneumoniae
Authors: Lazarova M / Frangakis A / Pos KM
History
DepositionMay 17, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50334.png

Downloads & links

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Map

FileDownload / File: emd_50334.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 380 pix.
= 318.06 Å		0.84 Å/pix.
x 380 pix.
= 318.06 Å		0.84 Å/pix.
x 380 pix.
= 318.06 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.272
Minimum - Maximum-0.55230314 - 1.2739031
Average (Standard dev.)0.0022266696 (±0.035595473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 318.06 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50334_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50334_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric Klebsiella pneumoniae efflux pump membrane transporter OqxB

EntireName: Trimeric Klebsiella pneumoniae efflux pump membrane transporter OqxB
Components
  • Complex: Trimeric Klebsiella pneumoniae efflux pump membrane transporter OqxB
    • Protein or peptide: Efflux pump membrane transporter

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Supramolecule #1: Trimeric Klebsiella pneumoniae efflux pump membrane transporter OqxB

SupramoleculeName: Trimeric Klebsiella pneumoniae efflux pump membrane transporter OqxB
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 343 KDa

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Macromolecule #1: Efflux pump membrane transporter

MacromoleculeName: Efflux pump membrane transporter / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 114.393211 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDFSRFFIDR PIFAAVLSIL IFITGLIAIP LLPVSEYPDV VPPSVQVRAE YPGANPKVIA ETVATPLEEA INGVENMMYM KSVAGSDGV LVTTVTFRPG TDPDQAQVQV QNRVAQAEAR LPEDVRRLGI TTQKQSPTLT LVVHLFSPNG KYDSLYMRNY A TLKVKDEL ...String:
MDFSRFFIDR PIFAAVLSIL IFITGLIAIP LLPVSEYPDV VPPSVQVRAE YPGANPKVIA ETVATPLEEA INGVENMMYM KSVAGSDGV LVTTVTFRPG TDPDQAQVQV QNRVAQAEAR LPEDVRRLGI TTQKQSPTLT LVVHLFSPNG KYDSLYMRNY A TLKVKDEL ARLPGVGQIQ IFGSGEYAMR VWLDPNKVAA RGLTASDVVT AMQEQNVQVS AGQLGAEPLP QESDFLISIN AQ GRLHTEE EFGNIILKTA QDGSLVRLRD VARIEMGSGS YALRSQLNNK DAVGIGIFQS PGANAIDLSN AVRAKMAELA TRF PEDMQW AAPYDPTVFV RDSIRAVVQT LLEAVVLVVL VVILFLQTWR ASIIPLIAVP VSVVGTFSIL YLLGFSLNTL SLFG LVLAI GIVVDDAIVV VENVERNIEE GLAPLAAAHQ AMREVSGPII AIALVLCAVF VPMAFLSGVT GQFYKQFAVT IAIST VISA INSLTLSPAL AALLLKPHGA KKDLPTRLID RLFGWIFRPF NRFFLRSSNG YQGLVSKTLG RRGAVFAVYL LLLCAA GVM FKVVPGGFIP TQDKLYLIGG VKMPEGSSLA RTDAVIRKMS EIGMNTEGVD YAVAFPGLNA LQFTNTPNTG TVFFGLK PF DQRKHTAAEI NAEINAKIAQ IQQGFGFSIL PPPILGLGQG SGYSLYIQDR GGLGYGALQS AVNAMSGAIM QTPGMHFP I STYQANVPQL DVQVDRDKAK AQGVSLTELF GTLQTYLGSS YVNDFNQFGR TWRVMAQADG PYRESVEDIA NLRTRNNQG EMVPIGSMVN ISTTYGPDPV IRYNGYPAAD LIGDADPRVL SSSQAMTHLE ELSKQILPNG MNIEWTDLSF QQATQGNTAL IVFPVAVLL AFLVLAALYE SWTLPLAVIL IVPMTMLSAL FGVWLTGGDN NVFVQVGLVV LMGLACKNAI LIVEFARELE I QGKGIMEA ALEACRLRLR PIVMTSIAFI AGTIPLILGH GAGAEVRGVT GITVFSGMLG VTLFGLFLTP VFYVTLRKLV TR RKPVQED LPAHHHHHH

UniProtKB: Efflux pump membrane transporter

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.7 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6562 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2703412
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 543928
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

PDB-9fdz:
Single particle cryo-EM structure of the multidrug efflux pump OqxB from Klebsiella pneumoniae

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