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- PDB-5nik: Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump -

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Basic information

Entry
Database: PDB / ID: 5nik
TitleStructure of the MacAB-TolC ABC-type tripartite multidrug efflux pump
Components
  • Macrolide export ATP-binding/permease protein MacB
  • Macrolide export protein MacA
  • Outer membrane protein TolC
KeywordsTRANSPORT PROTEIN / ABC transporter / drug efflux pump / multi-drug resistance / macrolide transporter / toxin transporter
Function / homology
Function and homology information


polymyxin transport / polymyxin transmembrane transporter activity / MacAB-TolC complex / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane ...polymyxin transport / polymyxin transmembrane transporter activity / MacAB-TolC complex / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / 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 / ABC-type xenobiotic transporter activity / bile acid and bile salt transport / porin activity / extrinsic component of membrane / efflux transmembrane transporter activity / transmembrane transporter activity / monoatomic ion channel activity / cell outer membrane / response to organic cyclic compound / response to toxic substance / outer membrane-bounded periplasmic space / monoatomic ion transmembrane transport / response to xenobiotic stimulus / response to antibiotic / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Macrolide export protein MacA / Macrolide export ATP-binding/permease protein macB family profile. / : / Type I secretion outer membrane protein, TolC / : / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / MacB-like periplasmic core domain ...Macrolide export protein MacA / Macrolide export ATP-binding/permease protein macB family profile. / : / Type I secretion outer membrane protein, TolC / : / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / MacB-like periplasmic core domain / MacB-like periplasmic core domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / Outer membrane efflux protein / Outer membrane efflux protein / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease family / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Outer membrane protein TolC / 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: 3.3 Å
AuthorsFitzpatrick, A.W.P. / Llabres, S. / Neuberger, A. / Blaza, J.N. / Bai, X.-C. / Okada, U. / Murakami, S. / van Veen, H.W. / Zachariae, U. / Scheres, S.H.W. ...Fitzpatrick, A.W.P. / Llabres, S. / Neuberger, A. / Blaza, J.N. / Bai, X.-C. / Okada, U. / Murakami, S. / van Veen, H.W. / Zachariae, U. / Scheres, S.H.W. / Luisi, B.F. / Du, D.
Funding support United Kingdom, Japan, 2items
OrganizationGrant numberCountry
Wellcome TrustRG61065 United Kingdom
Human Frontier Science ProgramRG68784 Japan
CitationJournal: Nat Microbiol / Year: 2017
Title: Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump.
Authors: Anthony W P Fitzpatrick / Salomé Llabrés / Arthur Neuberger / James N Blaza / Xiao-Chen Bai / Ui Okada / Satoshi Murakami / Hendrik W van Veen / Ulrich Zachariae / Sjors H W Scheres / Ben ...Authors: Anthony W P Fitzpatrick / Salomé Llabrés / Arthur Neuberger / James N Blaza / Xiao-Chen Bai / Ui Okada / Satoshi Murakami / Hendrik W van Veen / Ulrich Zachariae / Sjors H W Scheres / Ben F Luisi / Dijun Du /
Abstract: The MacA-MacB-TolC assembly of Escherichia coli is a transmembrane machine that spans the cell envelope and actively extrudes substrates, including macrolide antibiotics and polypeptide virulence ...The MacA-MacB-TolC assembly of Escherichia coli is a transmembrane machine that spans the cell envelope and actively extrudes substrates, including macrolide antibiotics and polypeptide virulence factors. These transport processes are energized by the ATPase MacB, a member of the ATP-binding cassette (ABC) superfamily. We present an electron cryo-microscopy structure of the ABC-type tripartite assembly at near-atomic resolution. A hexamer of the periplasmic protein MacA bridges between a TolC trimer in the outer membrane and a MacB dimer in the inner membrane, generating a quaternary structure with a central channel for substrate translocation. A gating ring found in MacA is proposed to act as a one-way valve in substrate transport. The MacB structure features an atypical transmembrane domain with a closely packed dimer interface and a periplasmic opening that is the likely portal for substrate entry from the periplasm, with subsequent displacement through an allosteric transport mechanism.
History
DepositionMar 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell / em_image_scans
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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Macrolide export protein MacA
E: Macrolide export protein MacA
F: Macrolide export protein MacA
G: Macrolide export protein MacA
H: Macrolide export protein MacA
I: Macrolide export protein MacA
J: Macrolide export ATP-binding/permease protein MacB
K: Macrolide export ATP-binding/permease protein MacB


Theoretical massNumber of molelcules
Total (without water)545,01411
Polymers545,01411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50040 Å2
ΔGint-200 kcal/mol
Surface area220920 Å2
MethodPISA

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Components

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


Mass: 52506.547 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: tolC, colE1-i, mtcB, mukA, refI, toc, weeA, b3035, JW5503
Production host: Escherichia coli (E. coli) / References: UniProt: P02930
#2: Protein
Macrolide export protein MacA


Mass: 40715.746 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: macA, ybjY, b0878, JW0862 / Production host: Escherichia coli (E. coli) / References: UniProt: P75830
#3: Protein Macrolide export ATP-binding/permease protein MacB


Mass: 71600.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: macB, ybjZ, b0879, JW0863 / Production host: Escherichia coli (E. coli)
References: UniProt: P75831, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

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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: MacAB-TolC / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 2 mg/ml / Embedding 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: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27614 / Symmetry type: POINT

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