5NAA | pdb_00005naa

Lipoprotein-releasing system transmembrane protein LolC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 
    0.225 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

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: https://doi.org/10.1073/pnas.1712153114
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 51.34 kDa 
  • Atom Count: 3,712 
  • Modeled Residue Count: 444 
  • Deposited Residue Count: 460 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipoprotein-releasing system transmembrane protein LolC
A, B
230Escherichia coli K-12Mutation(s): 0 
Gene Names: lolCycfUb1116JW5161
Membrane Entity: Yes 
UniProt
Find proteins for P0ADC3 (Escherichia coli (strain K12))
Explore P0ADC3 
Go to UniProtKB:  P0ADC3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADC3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free:  0.225 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.68α = 90
b = 111.78β = 108.97
c = 75.939γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2017-11-15 
  • Deposition Author(s): Kaplan, E.

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
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description