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- PDB-9qgy: Structure of the YbjP lipoprotein bound to the MacAB-TolC tripart... -

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Basic information

Entry
Database: PDB / ID: 9qgy
TitleStructure of the YbjP lipoprotein bound to the MacAB-TolC tripartite efflux pump
Components
  • (Macrolide export ...) x 2
  • Outer membrane protein TolC
  • Uncharacterized lipoprotein YbjP
KeywordsMEMBRANE PROTEIN / multi-drug efflux pump / MacAB-TolC / AcrABZ-TolC / type I secretion / lipoprotein / membrane protein assembly
Function / homology
Function and homology information


polymyxin transport / polymyxin transmembrane transporter activity / MacAB-TolC complex / 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 ...polymyxin transport / polymyxin transmembrane transporter activity / MacAB-TolC complex / 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 / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / extrinsic component of membrane / Antimicrobial resistance / ABC-type xenobiotic transporter activity / bile acid and bile salt transport / porin activity / Secretion of toxins / efflux transmembrane transporter activity / transmembrane transporter activity / monoatomic ion channel activity / cell outer membrane / response to toxic substance / monoatomic ion transmembrane transport / response to xenobiotic stimulus / response to antibiotic / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Macrolide export protein MacA / Domain of unknown function DUF3828 / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Protein of unknown function (DUF3828) / Macrolide export ATP-binding/permease protein macB family profile. / : / : / : / Type I secretion outer membrane protein, TolC / : ...Macrolide export protein MacA / Domain of unknown function DUF3828 / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Protein of unknown function (DUF3828) / Macrolide export ATP-binding/permease protein macB family profile. / : / : / : / Type I secretion outer membrane protein, TolC / : / RND efflux pump, membrane fusion protein / Outer membrane efflux protein / Outer membrane efflux protein / MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
(2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / Outer membrane protein TolC / Uncharacterized lipoprotein YbjP / Macrolide export protein MacA / Macrolide export ATP-binding/permease protein MacB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsKaplan, E. / Horne, J. / Luisi, B.F.
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 MacAB-TolC tripartite efflux pump
Authors: Kaplan, E. / Horne, J. / Luisi, B.F.
History
DepositionMar 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 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: Uncharacterized lipoprotein YbjP
E: Uncharacterized lipoprotein YbjP
F: Uncharacterized lipoprotein YbjP
G: Macrolide export protein MacA
H: Macrolide export protein MacA
I: Macrolide export protein MacA
J: Macrolide export protein MacA
K: Macrolide export protein MacA
L: Macrolide export protein MacA
M: Macrolide export ATP-binding/permease protein MacB
N: Macrolide export ATP-binding/permease protein MacB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)498,05920
Polymers496,24614
Non-polymers1,8136
Water39622
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 ABCDEF

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


Mass: 51495.555 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
#2: Protein Uncharacterized lipoprotein YbjP


Mass: 17004.725 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Lipid modified at N-termina cysteine / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ybjP, b0865, JW0849 / Production host: Escherichia coli (E. coli) / References: UniProt: P75818

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Macrolide export ... , 2 types, 8 molecules GHIJKLMN

#3: Protein
Macrolide export protein MacA


Mass: 40672.785 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: MacA hexamer / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: macA, ybjY, b0878, JW0862 / Production host: Escherichia coli (E. coli) / References: UniProt: P75830
#4: Protein Macrolide export ATP-binding/permease protein MacB


Mass: 23354.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: segment of MacB / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: macB, ybjZ, b0879, JW0863 / Production host: Escherichia coli (E. coli)
References: UniProt: P75831, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate

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Non-polymers , 3 types, 28 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-Z41 / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate


Mass: 568.911 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H68O5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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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, lipoprotein YbjP, MacA and the resolved portion of the ABC transporter MacB
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
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: 2700 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 49.75 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.20.1_4487model refinement
11cryoSPARCfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 233775 / Symmetry type: POINT
RefinementHighest resolution: 2.48 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00332910
ELECTRON MICROSCOPYf_angle_d0.69244649
ELECTRON MICROSCOPYf_dihedral_angle_d7.1244639
ELECTRON MICROSCOPYf_chiral_restr0.0445232
ELECTRON MICROSCOPYf_plane_restr0.0185918

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