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- EMDB-55890: Structure of the YbjP lipoprotein bound to the AcrABZ-TolC efflux pump -

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Basic information

Entry
Database: EMDB / ID: EMD-55890
TitleStructure of the YbjP lipoprotein bound to the AcrABZ-TolC efflux pump
Map data
Sample
  • Complex: Complex of TolC outer membrane protein, AcrA, AcrB and AcrZ bound to lipoprotein YbjP
    • Protein or peptide: Outer membrane protein TolC
    • Protein or peptide: Multidrug efflux pump subunit AcrA
    • Protein or peptide: Multidrug efflux pump subunit AcrB
    • Protein or peptide: Multidrug efflux pump accessory protein AcrZ
    • Protein or peptide: Uncharacterized lipoprotein YbjP
  • Ligand: CHLORIDE ION
KeywordsMulti-drug efflux pump / RND transporter / MacAB-TolC / AcrABZ-TolC / type I secretion / lipoprotein / membrane protein assembly / MEMBRANE PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


MacAB-TolC complex / alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / Iron assimilation using enterobactin / bile acid transmembrane transporter activity ...MacAB-TolC complex / alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / Iron assimilation using enterobactin / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / Antimicrobial resistance / bile acid and bile salt transport / porin activity / Secretion of toxins / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / monoatomic ion channel activity / fatty acid transport / xenobiotic transport / cell outer membrane / response to toxic substance / outer membrane-bounded periplasmic space / monoatomic ion transmembrane transport / response to xenobiotic stimulus / response to antibiotic / membrane / identical protein binding / plasma membrane
Similarity search - Function
Domain of unknown function DUF3828 / : / Protein of unknown function (DUF3828) / : / Multidrug efflux pump accessory protein AcrZ / Multidrug efflux pump-associated protein AcrZ / : / : / : / RND MFP, alpha-helical hairpin domain ...Domain of unknown function DUF3828 / : / Protein of unknown function (DUF3828) / : / Multidrug efflux pump accessory protein AcrZ / Multidrug efflux pump-associated protein AcrZ / : / : / : / RND MFP, alpha-helical hairpin domain / RND MFPs, beta-barrel domain / Type I secretion outer membrane protein, TolC / : / : / RND MFPs, C-terminal permuted SH3 domain / : / RND MFP, barrel-sandwich hybrid domain / RND efflux pump, membrane fusion protein / Outer membrane efflux protein / Outer membrane efflux protein / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Outer membrane protein TolC / Multidrug efflux pump accessory protein AcrZ / Multidrug efflux pump subunit AcrA / Multidrug efflux pump subunit AcrB / Uncharacterized lipoprotein YbjP
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsHarris A / Horne J / Kaplan E / Petsolari E / Luisi B
Funding support United Kingdom, European Union, 2 items
OrganizationGrant numberCountry
Wellcome Trust222451/Z/21/Z United Kingdom
European Research Council (ERC)742210European Union
CitationJournal: To Be Published
Title: Structure of the YbjP lipoprotein bound to the AcrABZ-TolC efflux pump
Authors: Kaplan E / Harris A / Horne J / Petsolari E / Luisi B
History
DepositionNov 28, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55890.png

Downloads & links

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Map

FileDownload / File: emd_55890.map.gz / Format: CCP4 / Size: 775.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 588 pix.
= 686.784 Å		1.17 Å/pix.
x 588 pix.
= 686.784 Å		1.17 Å/pix.
x 588 pix.
= 686.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.168 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.17887786 - 0.55078727
Average (Standard dev.)0.000119435426 (±0.0096827485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions588588588
Spacing588588588
CellA=B=C: 686.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55890_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55890_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55890_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 : Complex of TolC outer membrane protein, AcrA, AcrB and AcrZ bound...

EntireName: Complex of TolC outer membrane protein, AcrA, AcrB and AcrZ bound to lipoprotein YbjP
Components
  • Complex: Complex of TolC outer membrane protein, AcrA, AcrB and AcrZ bound to lipoprotein YbjP
    • Protein or peptide: Outer membrane protein TolC
    • Protein or peptide: Multidrug efflux pump subunit AcrA
    • Protein or peptide: Multidrug efflux pump subunit AcrB
    • Protein or peptide: Multidrug efflux pump accessory protein AcrZ
    • Protein or peptide: Uncharacterized lipoprotein YbjP
  • Ligand: CHLORIDE ION

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Supramolecule #1: Complex of TolC outer membrane protein, AcrA, AcrB and AcrZ bound...

SupramoleculeName: Complex of TolC outer membrane protein, AcrA, AcrB and AcrZ bound to lipoprotein YbjP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)

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Macromolecule #1: Outer membrane protein TolC

MacromoleculeName: Outer membrane protein TolC / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 52.623715 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MENLMQVYQQ ARLSNPELRK SAADRDAAFE KINEARSPLL PQLGLGADYT YSNGYRDANG INSNATSASL QLTQSIFDMS KWRALTLQE KAAGIQDVTY QTDQQTLILN TATAYFNVLN AIDVLSYTQA QKEAIYRQLD QTTQRFNVGL VAITDVQNAR A QYDTVLAN ...String:
MENLMQVYQQ ARLSNPELRK SAADRDAAFE KINEARSPLL PQLGLGADYT YSNGYRDANG INSNATSASL QLTQSIFDMS KWRALTLQE KAAGIQDVTY QTDQQTLILN TATAYFNVLN AIDVLSYTQA QKEAIYRQLD QTTQRFNVGL VAITDVQNAR A QYDTVLAN EVTARNNLDN AVEQLRQITG NYYPELAALN VENFKTDKPQ PVNALLKEAE KRNLSLLQAR LSQDLAREQI RQ AQDGHLP TLDLTASTGI SDTSYSGSKT RGAAGTQYDD SNMGQNKVGL SFSLPIYQGG MVNSQVKQAQ YNFVGASEQL ESA HRSVVQ TVRSSFNNIN ASISSINAYK QAVVSAQSSL DAMEAGYSVG TRTIVDVLDA TTTLYNAKQE LANARYNYLI NQLN IKSAL GTLNEQDLLA LNNALSKPVS TNPENVAPQT PEQNAIADGY APDSPAPVVQ QTSARTTTSN GHNPFRNDYK DDDDK

UniProtKB: Outer membrane protein TolC

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Macromolecule #2: Multidrug efflux pump subunit AcrA

MacromoleculeName: Multidrug efflux pump subunit AcrA / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 42.237488 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNKNRGFTPL AVVLMLSGSL ALTGCDDKQA QQGGQQMPAV GVVTVKTEPL QITTELPGRT SAYRIAEVRP QVSGIILKRN FKEGSDIEA GVSLYQIDPA TYQATYDSAK GDLAKAQAAA NIAQLTVNRY QKLLGTQYIS KQEYDQALAD AQQANAAVTA A KAAVETAR ...String:
MNKNRGFTPL AVVLMLSGSL ALTGCDDKQA QQGGQQMPAV GVVTVKTEPL QITTELPGRT SAYRIAEVRP QVSGIILKRN FKEGSDIEA GVSLYQIDPA TYQATYDSAK GDLAKAQAAA NIAQLTVNRY QKLLGTQYIS KQEYDQALAD AQQANAAVTA A KAAVETAR INLAYTKVTS PISGRIGKSN VTEGALVQNG QATALATVQQ LDPIYVDVTQ SSNDFLRLKQ ELANGTLKQE NG KAKVSLI TSDGIKFPQD GTLEFSDVTV DQTTGSITLR AIFPNPDHTL LPGMFVRARL EEGLNPNAIL VPQQGVTRTP RGD ATVLVV GADDKVETRP IVASQAIGDK WLVTEGLKAG DRVVISGLQK VRPGVQVKAQ EVTADNNQQA ASGAQPEQSK S

UniProtKB: Multidrug efflux pump subunit AcrA

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Macromolecule #3: Multidrug efflux pump subunit AcrB

MacromoleculeName: Multidrug efflux pump subunit AcrB / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 113.66518 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPNFFIDRPI FAWVIAIIIM LAGGLAILKL PVAQYPTIAP PAVTISASYP GADAKTVQDT VTQVIEQNMN GIDNLMYMSS NSDSTGTVQ ITLTFESGTD ADIAQVQVQN KLQLAMPLLP QEVQQQGVSV EKSSSSFLMV VGVINTDGTM TQEDISDYVA A NMKDAISR ...String:
MPNFFIDRPI FAWVIAIIIM LAGGLAILKL PVAQYPTIAP PAVTISASYP GADAKTVQDT VTQVIEQNMN GIDNLMYMSS NSDSTGTVQ ITLTFESGTD ADIAQVQVQN KLQLAMPLLP QEVQQQGVSV EKSSSSFLMV VGVINTDGTM TQEDISDYVA A NMKDAISR TSGVGDVQLF GSQYAMRIWM NPNELNKFQL TPVDVITAIK AQNAQVAAGQ LGGTPPVKGQ QLNASIIAQT RL TSTEEFG KILLKVNQDG SRVLLRDVAK IELGGENYDI IAEFNGQPAS GLGIKLATGA NALDTAAAIR AELAKMEPFF PSG LKIVYP YDTTPFVKIS IHEVVKTLVE AIILVFLVMY LFLQNFRATL IPTIAVPVVL LGTFAVLAAF GFSINTLTMF GMVL AIGLL VDDAIVVVEN VERVMAEEGL PPKEATRKSM GQIQGALVGI AMVLSAVFVP MAFFGGSTGA IYRQFSITIV SAMAL SVLV ALILTPALCA TMLKPIAKGD HGEGKKGFFG WFNRMFEKST HHYTDSVGGI LRSTGRYLVL YLIIVVGMAY LFVRLP SSF LPDEDQGVFM TMVQLPAGAT QERTQKVLNE VTHYYLTKEK NNVESVFAVN GFGFAGRGQN TGIAFVSLKD WADRPGE EN KVEAITMRAT RAFSQIKDAM VFAFNLPAIV ELGTATGFDF ELIDQAGLGH EKLTQARNQL LAEAAKHPDM LTSVRPNG L EDTPQFKIDI DQEKAQALGV SINDINTTLG AAWGGSYVND FIDRGRVKKV YVMSEAKYRM LPDDIGDWYV RAADGQMVP FSAFSSSRWE YGSPRLERYN GLPSMEILGQ AAPGKSTGEA MELMEQLASK LPTGVGYDWT GMSYQERLSG NQAPSLYAIS LIVVFLCLA ALYESWSIPF SVMLVVPLGV IGALLAATFR GLTNDVYFQV GLLTTIGLSA KNAILIVEFA KDLMDKEGKG L IEATLDAV RMRLRPILMT SLAFILGVMP LVISTGAGSG AQNAVGTGVM GGMVTATVLA IFFVPVFFVV VRRRFSRKNE DI EHSHTVD HH

UniProtKB: Multidrug efflux pump subunit AcrB

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Macromolecule #4: Multidrug efflux pump accessory protein AcrZ

MacromoleculeName: Multidrug efflux pump accessory protein AcrZ / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 5.304423 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLELLKSLVF AVIMVPVVMA IILGLIYGLG EVFNIFSGVG KKDQPGQNH

UniProtKB: Multidrug efflux pump accessory protein AcrZ

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Macromolecule #5: Uncharacterized lipoprotein YbjP

MacromoleculeName: Uncharacterized lipoprotein YbjP / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.122873 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDNGTRSGPC VEGGPDNVAQ QFYDYRILHR SNDITALRPY LSDKLATLLS DASRDNNHRE LLTNDPFSSR TTLPDSAHVA SASTIPNRD ARNIPLRVDL KQGDQGWQDE VLMIQEGQCW VIDDVRYLGG SVHATAGTLR QSIENRENLY FQSLEHHHHH H

UniProtKB: Uncharacterized lipoprotein YbjP

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Macromolecule #6: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ng5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: Coot (ver. 0.9.8.1), PHENIX (ver. 1.20.1)) / Number images used: 97441
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: Coot
Output model

PDB-9tg4:
Structure of the YbjP lipoprotein bound to the AcrABZ-TolC efflux pump

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