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- EMDB-18777: Single particle cryo-EM co-structure of Klebsiella pneumoniae Acr... -

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Basic information

Entry
Database: EMDB / ID: EMD-18777
TitleSingle particle cryo-EM co-structure of Klebsiella pneumoniae AcrB with the BDM91288 efflux pump inhibitor at 3.42 Angstrom resolution
Map data
Sample
  • Complex: Trimeric Klebsiella pneumoniae AcrB with BDM91288 efflux pump inhibitor
    • Protein or peptide: Efflux pump membrane transporter
  • Ligand: 3-chloranyl-2,6-di(piperazin-4-ium-1-yl)quinoline
KeywordsEfflux Pump Inhibitor / Transmembrane Binding / Antibiotic Resistance / TRANSPORT PROTEIN
Function / homology:
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsBoernsen C / Mueller RT / Pos KM / Frangakis AS
Funding support Germany, France, 2 items
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 RT
History
DepositionOct 27, 2023-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18777.png

Downloads & links

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Map

FileDownload / File: emd_18777.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: 0.24
Minimum - Maximum-1.2859604 - 1.8314655
Average (Standard dev.)0.0038945402 (±0.05781421)
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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Mask #1

Fileemd_18777_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18777_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_18777_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 AcrB with BDM91288 efflux pump inh...

EntireName: Trimeric Klebsiella pneumoniae AcrB with BDM91288 efflux pump inhibitor
Components
  • Complex: Trimeric Klebsiella pneumoniae AcrB with BDM91288 efflux pump inhibitor
    • Protein or peptide: Efflux pump membrane transporter
  • Ligand: 3-chloranyl-2,6-di(piperazin-4-ium-1-yl)quinoline

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Supramolecule #1: Trimeric Klebsiella pneumoniae AcrB with BDM91288 efflux pump inh...

SupramoleculeName: Trimeric Klebsiella pneumoniae AcrB with BDM91288 efflux pump inhibitor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Klebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940 (bacteria)
Strain: FDAARGOS_775

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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 subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940 (bacteria)
Strain: FDAARGOS_775
Molecular weightTheoretical: 114.489945 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPNFFIDRPI FAWVIAIIIM LAGGLSILKL PVAQYPTIAP PAISITAMYP GADAETVQNT VTQVIEQNMN GIDHLMYMSS NGDSTGTAT ITLTFESGTD PDIAQVQVQN KLALATPLLP QEVQQQGISV EKASSSFLMV VGVINTNGTM NQDDISDYVA A NMKDPISR ...String:
MPNFFIDRPI FAWVIAIIIM LAGGLSILKL PVAQYPTIAP PAISITAMYP GADAETVQNT VTQVIEQNMN GIDHLMYMSS NGDSTGTAT ITLTFESGTD PDIAQVQVQN KLALATPLLP QEVQQQGISV EKASSSFLMV VGVINTNGTM NQDDISDYVA A NMKDPISR TSGVGDVQLF GSQYAMRIWM DPNKLNNFQL TPVDVISALK AQNAQVAAGQ LGGTPPVKGQ QLNASIIAQT RL TNTEEFG NILLKVNQDG SQVRLRDVAK IELGGESYDV VAKFNGQPAS GLGIKLATGA NALDTANAIR AELAKMEPFF PSG MKIVYP YDTTPFVKIS IHEVVKTLVE AIILVFLVMY LFLQNFRATL IPTIAVPVVL LGTFAVLAAF GFSINTLTMF GMVL AIGLL VDDAIVVVEN VERVMAEEGL PPKEATRKSM GQIQGALVGI AMVLSAVFIP MAFFGGSTGA IYRQFSITIV SAMAL SVLV ALILTPALCA TMLKPIQKGS HGATTGFFGW FNRMFDKSTH HYTDSVGNIL RSTGRYLVLY LIIVVGMAWL FVRLPS SFL PDEDQGVFLS MAQLPAGATQ ERTQKVLDEM TNYYLTKEKD NVESVFAVNG FGFAGRGQNT GIAFVSLKDW SQRPGEE NK VEAITARAMG YFSQIKDAMV FAFNLPAIVE LGTATGFDFE LIDQGGLGHE KLTQARNQLF GMVAQHPDVL TGVRPNGL E DTPQFKIDID QEKAQALGVS ISDINTTLGA AWGGSYVNDF IDRGRVKKVY IMSEAKYRML PEDIGKWYVR GSDGQMVPF SAFSTSRWEY GSPRLERYNG LPSLEILGQA APGKSTGEAM ALMEELAGKL PSGIGYDWTG MSYQERLSGN QAPALYAISL IVVFLCLAA LYESWSIPFS VMLVVPLGVV GALLAATFRG LTNDVYFQVG LLTTIGLSAK NAILIVEFAK DLMEKEGKGL I EATLEAVR MRLRPILMTS LAFILGVMPL VISSGAGSGA QNAVGTGVMG GMVTATILAI FFVPVFFVVV RRRFSKKTED IE HSHQVEH HLEHHHHHH

UniProtKB: UNIPROTKB: J2LW81

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Macromolecule #2: 3-chloranyl-2,6-di(piperazin-4-ium-1-yl)quinoline

MacromoleculeName: 3-chloranyl-2,6-di(piperazin-4-ium-1-yl)quinoline / type: ligand / ID: 2 / Number of copies: 2 / Formula: WQW
Molecular weightTheoretical: 333.859 Da
Chemical component information

ChemComp-WQW:
3-chloranyl-2,6-di(piperazin-4-ium-1-yl)quinoline

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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

Concentration4.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMsodium chlorideNaCl
0.02 %DDM
GridMaterial: COPPER
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 Quantum SE / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8487 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.5 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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: 380181
Startup modelType of model: NONE
Final reconstructionNumber classes used: 2 / Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 109174
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8qzl:
Single particle cryo-EM co-structure of Klebsiella pneumoniae AcrB with the BDM91288 efflux pump inhibitor at 3.42 Angstrom resolution

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