2RDD

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

• PDB DOI: https://doi.org/10.2210/pdb2RDD/pdb

• Classification: Membrane protein/TRANSPORT PROTEIN
• Organism(s): Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2007-09-22 Released: 2007-12-11 
• Deposition Author(s): Tornroth-Horsefield, S., Gourdon, P., Horsefield, R., Neutze, R.

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 18073115 
• 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.

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Organizational Affiliation: 

Department of Chemistry, Biochemistry and Biophysics, Gothenburg University, 40530 Gothenburg, Sweden. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 118.81 kDa 
• Atom Count: 8,026 
• Modelled Residue Count: 1,055 
• Deposited Residue Count: 1,086 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acriflavine resistance protein B	A	1,049	Escherichia coli	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224  Go to UniProtKB:  P31224

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0092 membrane protein yajC	B	37	Escherichia coli	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0ADZ7 (Escherichia coli (strain K12)) Explore P0ADZ7  Go to UniProtKB:  P0ADZ7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AIC	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 = 145.097	α = 90
b = 145.097	β = 90
c = 511.644	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-11 
Deposition Author(s): Tornroth-Horsefield, S., Gourdon, P., Horsefield, R., Neutze, R.

Revision History  

• 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