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

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Basic information

Entry
Database: PDB / ID: 9tg4
TitleStructure of the YbjP lipoprotein bound to the AcrABZ-TolC efflux pump
Components
  • (Multidrug efflux pump subunit ...) x 2
  • Multidrug efflux pump accessory protein AcrZ
  • Outer membrane protein TolC
  • Uncharacterized lipoprotein YbjP
KeywordsTRANSPORT PROTEIN / Multi-drug efflux pump / RND transporter / MacAB-TolC / AcrABZ-TolC / type I secretion / lipoprotein / membrane protein assembly / MEMBRANE 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 / efflux pump complex / periplasmic side of plasma membrane / 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 / efflux pump complex / periplasmic side of plasma membrane / Iron assimilation using enterobactin / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / Antimicrobial resistance / porin activity / xenobiotic transport / Secretion of toxins / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / monoatomic ion channel activity / bile acid and bile salt transport / cell outer membrane / response to toxic substance / outer membrane-bounded periplasmic space / monoatomic ion transmembrane transport / response to antibiotic / response to xenobiotic stimulus / 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 (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsKaplan, E. / Harris, A. / Horne, J. / Petsolari, E. / Luisi, B.
Funding support United Kingdom, European Union, 2items
OrganizationGrant numberCountry
Wellcome Trust222451/Z/21/Z United Kingdom
European Research Council (ERC)742210European Union
CitationJournal: Elife / Year: 2026
Title: A lipoprotein partner for the outer membrane protein TolC.
Authors: Jim Horne / Elise Kaplan / Ben Jin / Kieran Abbott / Victor Flores / Emmanouela Petsolari / Jan Gradon / Yvette Ntsogo / Andrzej Harris / Dingquan Yu / Ashraf Zarkan / Ben F Luisi /
Abstract: The outer membrane protein TolC from belongs to an extensive superfamily whose members are found throughout the didermal, Gram-negative bacterial lineages. The protein serves as an activated exit ...The outer membrane protein TolC from belongs to an extensive superfamily whose members are found throughout the didermal, Gram-negative bacterial lineages. The protein serves as an activated exit duct in multi-drug efflux pumps and protein secretion machinery. Many TolC homologues bear a lipid modification on the N-terminus that embeds into the inner leaflet of the outer membrane and appears to have been a conserved feature; however, the moiety is absent entirely in the TolC. We have discovered that the lipoprotein YbjP interacts extensively with the periplasmic surface of TolC and its N-terminal lipid moiety is embedded in the membrane, mimicking the intramolecular and modification-membrane interactions seen in TolC homologues. Here, we present cryo-EM structures of the MacA-MacB-TolC and AcrA-AcrB-TolC tripartite pumps complexed to YbjP. Although the association occurs spontaneously both in vitro and in vivo, the YbjP-TolC interaction is not required for efflux activity under standard laboratory conditions. YbjP may contribute to stabilising the orientation and distribution of TolC in the outer membrane, as well as the expression of transporters for tryptophan and cyclic peptide toxins.
History
DepositionNov 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein TolC
B: Outer membrane protein TolC
C: Outer membrane protein TolC
D: Multidrug efflux pump subunit AcrA
E: Multidrug efflux pump subunit AcrA
F: Multidrug efflux pump subunit AcrA
G: Multidrug efflux pump subunit AcrA
H: Multidrug efflux pump subunit AcrA
I: Multidrug efflux pump subunit AcrA
J: Multidrug efflux pump subunit AcrB
K: Multidrug efflux pump subunit AcrB
L: Multidrug efflux pump subunit AcrB
M: Multidrug efflux pump accessory protein AcrZ
N: Multidrug efflux pump accessory protein AcrZ
O: Multidrug efflux pump accessory protein AcrZ
P: Uncharacterized lipoprotein YbjP
Q: Uncharacterized lipoprotein YbjP
R: Uncharacterized lipoprotein YbjP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)822,68021
Polymers822,57418
Non-polymers1063
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

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Protein , 2 types, 6 molecules ABCPQR

#1: Protein Outer membrane protein TolC / Multidrug efflux pump subunit TolC / Outer membrane factor TolC


Mass: 52623.715 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: tolC, colE1-i, mtcB, mukA, refI, toc, weeA, b3035, JW5503
Production host: Escherichia coli (E. coli) / References: UniProt: P02930
#5: Protein Uncharacterized lipoprotein YbjP


Mass: 18122.873 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ybjP, b0865, JW0849 / Production host: Escherichia coli (E. coli) / References: UniProt: P75818

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Multidrug efflux pump subunit ... , 2 types, 9 molecules DEFGHIJKL

#2: Protein
Multidrug efflux pump subunit AcrA / AcrAB-TolC multidrug efflux pump subunit AcrA / Acridine resistance protein A


Mass: 42237.488 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acrA, lir, mtcA, b0463, JW0452 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AE06
#3: Protein Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 113665.180 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acrB, acrE, b0462, JW0451 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224

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Protein/peptide / Non-polymers , 2 types, 6 molecules MNO

#4: Protein/peptide Multidrug efflux pump accessory protein AcrZ / AcrAB-TolC multidrug efflux pump accessory protein AcrZ / Acridine resistance protein Z


Mass: 5304.423 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acrZ, ybhT, b0762, JW5102 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AAW9
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl

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Details

Has ligand of interestN
Has protein modificationY

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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: Complex of TolC outer membrane protein, AcrA, AcrB and AcrZ bound to lipoprotein YbjP
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Source (recombinant)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7Cootmodel fitting
12Coot0.9.8.13D reconstruction
13PHENIX1.20.13D reconstruction
14PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97441 / Symmetry type: POINT
RefinementHighest resolution: 3.17 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00454504
ELECTRON MICROSCOPYf_angle_d0.56374060
ELECTRON MICROSCOPYf_dihedral_angle_d4.3937552
ELECTRON MICROSCOPYf_chiral_restr0.0468753
ELECTRON MICROSCOPYf_plane_restr0.0049654

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