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- PDB-5o66: Asymmetric AcrABZ-TolC -

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Basic information

Entry
Database: PDB / ID: 5o66
TitleAsymmetric AcrABZ-TolC
Components
  • Multidrug efflux pump accessory protein AcrZ
  • Multidrug efflux pump subunit AcrA
  • Multidrug efflux pump subunit AcrB
  • Outer membrane protein TolC
KeywordsMEMBRANE PROTEIN / multidrug efflux pump / membrane transporter
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 / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane ...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 / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transport / bile acid and bile salt transport / porin activity / monoatomic ion channel activity / efflux transmembrane transporter activity / transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / cell outer membrane / response to toxic substance / outer membrane-bounded periplasmic space / monoatomic ion transmembrane transport / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Multidrug efflux pump accessory protein AcrZ / Multidrug efflux pump-associated protein AcrZ / : / Type I secretion outer membrane protein, TolC / : / Cation efflux system protein CusB, domain 1 / : / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain ...: / Multidrug efflux pump accessory protein AcrZ / Multidrug efflux pump-associated protein AcrZ / : / Type I secretion outer membrane protein, TolC / : / Cation efflux system protein CusB, domain 1 / : / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / : / 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
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
Escherichia coli O157:H7 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsDu, D. / Luisi, B.F.
Funding support United Kingdom, Japan, 2items
OrganizationGrant numberCountry
Wellcome TrustRG61065 United Kingdom
HFSPRG68784 Japan
CitationJournal: Elife / Year: 2017
Title: An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump.
Authors: Zhao Wang / Guizhen Fan / Corey F Hryc / James N Blaza / Irina I Serysheva / Michael F Schmid / Wah Chiu / Ben F Luisi / Dijun Du /
Abstract: Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell ...Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell envelope. Here, we report the near-atomic resolution cryoEM structures of the AcrAB-TolC multidrug efflux pump in resting and drug transport states, revealing a quaternary structural switch that allosterically couples and synchronizes initial ligand binding with channel opening. Within the transport-activated state, the channel remains open even though the pump cycles through three distinct conformations. Collectively, our data provide a dynamic mechanism for the assembly and operation of the AcrAB-TolC pump.
History
DepositionJun 5, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionJun 14, 2017ID: 5V78
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: em_image_scans / pdbx_validate_close_contact / struct_conn
Revision 1.2Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jul 2, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details / Item: _em_software.name

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Structure visualization

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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


Theoretical massNumber of molelcules
Total (without water)759,13515
Polymers759,13515
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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


Mass: 53783.355 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria)
Gene: tolC, colE1-i, mtcB, mukA, refI, toc, weeA, b3035, JW5503
Production host: Escherichia coli (E. coli) / References: UniProt: P02930
#2: Protein
Multidrug efflux pump subunit AcrA / AcrAB-TolC multidrug efflux pump subunit AcrA / Acriflavine resistance protein A


Mass: 39800.660 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: acrA, Z0578, ECs0516 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AE07
#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 K12 (bacteria) / Gene: acrB, acrE, b0462, JW0451 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224
#4: Protein Multidrug efflux pump accessory protein AcrZ / AcrAB-TolC multidrug efflux pump accessory protein AcrZ / Acridine resistance protein Z


Mass: 5995.157 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: acrZ, Z0932, ECs0790 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AAX1
Has protein modificationN

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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

Component
IDNameTypeEntity IDParent-IDSource
1AcrABZ-TolCCOMPLEXall0MULTIPLE SOURCES
2AcrABZ-TolCCOMPLEX#1, #31RECOMBINANT
3AcrABZ-TolCCOMPLEX#2, #41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli K12 (bacteria)83333
33Escherichia coli O157:H7 (bacteria)83334
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.6
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26950 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00875398
ELECTRON MICROSCOPYf_angle_d0.981125159
ELECTRON MICROSCOPYf_dihedral_angle_d11.52446447
ELECTRON MICROSCOPYf_chiral_restr0.0498126
ELECTRON MICROSCOPYf_plane_restr0.00512235

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