2RDD

X-ray crystal structure of AcrB in complex with a novel transmembrane helix.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.279 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of AcrB in complex with a single transmembrane subunit reveals another twist.

Tornroth-Horsefield, S.Gourdon, P.Horsefield, R.Brive, L.Yamamoto, N.Mori, H.Snijder, A.Neutze, R.

(2007) Structure 15: 1663-1673

  • DOI: https://doi.org/10.1016/j.str.2007.09.023
  • Primary Citation of Related Structures:  
    2RDD

  • PubMed Abstract: 

    Bacterial drug resistance is a serious concern for human health. Multidrug efflux pumps export a broad variety of substrates out of the cell and thereby convey resistance to the host. In Escherichia coli, the AcrB:AcrA:TolC efflux complex forms a principal transporter for which structures of the individual component proteins have been determined in isolation. Here, we present the X-ray structure of AcrB in complex with a single transmembrane protein, assigned by mass spectrometry as YajC. A specific rotation of the periplasmic porter domain of AcrB is also revealed, consistent with the hypothesized "twist-to-open" mechanism for TolC activation. Growth experiments with yajc-deleted E. coli reveal a modest increase in the organism's susceptibility to beta-lactam antibiotics, but this effect could not conclusively be attributed to the loss of interactions between YajC and AcrB.


  • Organizational Affiliation

    Department of Chemistry, Biochemistry and Biophysics, Gothenburg University, 40530 Gothenburg, Sweden. susanna.tornroth@chem.gu.se


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acriflavine resistance protein B1,049Escherichia coliMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P31224 (Escherichia coli (strain K12))
Explore P31224 
Go to UniProtKB:  P31224
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31224
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0092 membrane protein yajC37Escherichia coliMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0ADZ7 (Escherichia coli (strain K12))
Explore P0ADZ7 
Go to UniProtKB:  P0ADZ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADZ7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AIC
Query on AIC

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
(2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
C16 H19 N3 O4 S
AVKUERGKIZMTKX-NJBDSQKTSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.279 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.097α = 90
b = 145.097β = 90
c = 511.644γ = 120
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description