5NIL | pdb_00005nil

Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump-MacB section

• PDB DOI: https://doi.org/10.2210/pdb5NIL/pdb
• EM Map EMD-3653: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2017-03-24 Released: 2017-05-24 
• Deposition Author(s): 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 Organization(s): Wellcome Trust, Human Frontier Science Program

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump.

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.

(2017) Nat Microbiol 2: 17070-17070

• PubMed: 28504659 
• DOI: https://doi.org/10.1038/nmicrobiol.2017.70
• Primary Citation Related Structures: 
  5NIK, 5NIL


• PubMed 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 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.

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Organizational Affiliation: 
• Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, U.K.
Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K.
Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K.
MRC Mitochondrial Biology Unit, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY.
Department of Life Science, Tokyo Institute of Technology, 4259-J2-17, Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, U.K.
Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 11-mer - A6B3C2 

Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 9-mer - A6B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 545.01 kDa 
• Atom Count: 35,215 
• Modeled Residue Count: 4,582 
• Deposited Residue Count: 4,971 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein TolC	A, B, C	479	Escherichia coli K-12	Mutation(s): 0  Gene Names: tolC, colE1-i, mtcB, mukA, refI, toc, weeA, b3035, JW5503 Membrane Entity: Yes
UniProt
Find proteins for P02930 (Escherichia coli (strain K12)) Explore P02930  Go to UniProtKB:  P02930

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrolide export protein MacA	D, E, F, G, H, I	371	Escherichia coli K-12	Mutation(s): 0  Gene Names: macA, ybjY, b0878, JW0862 Membrane Entity: Yes
UniProt
Find proteins for P75830 (Escherichia coli (strain K12)) Explore P75830  Go to UniProtKB:  P75830

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrolide export ATP-binding/permease protein MacB	J, K	654	Escherichia coli K-12	Mutation(s): 0  Gene Names: macB, ybjZ, b0879, JW0863 EC: 3.6.3 (PDB Primary Data), 7.6.2 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P75831 (Escherichia coli (strain K12)) Explore P75831  Go to UniProtKB:  P75831

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	RG61065
Human Frontier Science Program	Japan	RG68784

Revision History  

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2019-10-23
  Changes: Data collection, Other
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references