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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 / 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 (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: 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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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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