5LJ6

Structure of Aggregatibacter actinomycetemcomitans MacB bound to ATPyS (P6522)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.270 

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Ligand Structure Quality Assessment 


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Literature

Structure and mechanotransmission mechanism of the MacB ABC transporter superfamily.

Crow, A., Greene, N.P., Kaplan, E., Koronakis, V.

(2017) Proc Natl Acad Sci U S A 114: 12572-12577

  • DOI: 10.1073/pnas.1712153114
  • Primary Citation of Related Structures:  
    5LIL, 5LJ6, 5LJ7, 5LJ8, 5LJ9, 5LJA, 5NAA

  • PubMed Abstract: 

    • MacB is an ABC transporter that collaborates with the MacA adaptor protein and TolC exit duct to drive efflux of antibiotics and enterotoxin STII out of the bacterial cell. Here we present the structure of ATP-bound MacB and reveal precise molecular details of its mechanism ...

    MacB is an ABC transporter that collaborates with the MacA adaptor protein and TolC exit duct to drive efflux of antibiotics and enterotoxin STII out of the bacterial cell. Here we present the structure of ATP-bound MacB and reveal precise molecular details of its mechanism. The MacB transmembrane domain lacks a central cavity through which substrates could be passed, but instead conveys conformational changes from one side of the membrane to the other, a process we term mechanotransmission. Comparison of ATP-bound and nucleotide-free states reveals how reversible dimerization of the nucleotide binding domains drives opening and closing of the MacB periplasmic domains via concerted movements of the second transmembrane segment and major coupling helix. We propose that the assembled tripartite pump acts as a molecular bellows to propel substrates through the TolC exit duct, driven by MacB mechanotransmission. Homologs of MacB that do not form tripartite pumps, but share structural features underpinning mechanotransmission, include the LolCDE lipoprotein trafficking complex and FtsEX cell division signaling protein. The MacB architecture serves as the blueprint for understanding the structure and mechanism of an entire ABC transporter superfamily and the many diverse functions it supports.

    Organizational Affiliation: 

    Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom vk103@cam.ac.uk.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Macrolide export ATP-binding/permease protein MacBA664Aggregatibacter actinomycetemcomitansMutation(s): 0 
Gene Names: macB
EC: 3.6.3 (PDB Primary Data), 7.6.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q2EHL8 (Aggregatibacter actinomycetemcomitans)
Explore Q2EHL8 
Go to UniProtKB:  Q2EHL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2EHL8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.270 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.57α = 90
b = 119.57β = 90
c = 307.779γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-07-18 
  • Released Date: 2017-11-15 
    • Deposition Author(s): Crow, A.
Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/N000994/1

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Database references