2GIF

Asymmetric structure of trimeric AcrB from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb2GIF/pdb

• Classification: MEMBRANE PROTEIN/TRANSPORT PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2006-03-28 Released: 2006-09-12 
• Deposition Author(s): Seeger, M.A., Schiefner, A., Eicher, T., Verrey, F., Diederichs, K., Pos, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.267 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 

Starting Model: experimental

Literature

Structural Asymmetry of AcrB Trimer Suggests a Peristaltic Pump Mechanism.

Seeger, M.A., Schiefner, A., Eicher, T., Verrey, F., Diederichs, K., Pos, K.M.

(2006) Science 313: 1295-1298

• PubMed: 16946072 
• DOI: https://doi.org/10.1126/science.1131542
• Primary Citation of Related Structures:  
  2GIF, 2HRT


• PubMed Abstract: 
  

  The AcrA/AcrB/TolC complex spans the inner and outer membranes of Escherichia coli and serves as its major drug-resistance pump. Driven by the proton motive force, it mediates the efflux of bile salts, detergents, organic solvents, and many structurally unrelated antibiotics. Here, we report a crystallographic structure of trimeric AcrB determined at 2.9 and 3.0 angstrom resolution in space groups that allow asymmetry of the monomers. This structure reveals three different monomer conformations representing consecutive states in a transport cycle. The structural data imply an alternating access mechanism and a novel peristaltic mode of drug transport by this type of transporter.

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Organizational Affiliation: 

Institute of Physiology and Zurich Centre for Integrative Human Physiology (ZIHP), University of Zurich, Winterthurerstrasse 190, Zürich, Switzerland.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 344.59 kDa 
• Atom Count: 23,650 
• Modelled Residue Count: 3,108 
• Deposited Residue Count: 3,171 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acriflavine resistance protein B	A, B, C	1,057	Escherichia coli	Mutation(s): 0  Gene Names: acrB, acrE Membrane Entity: Yes
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224  Go to UniProtKB:  P31224

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	D [auth A], E [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.267 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 222.8	α = 90
b = 134.1	β = 98.21
c = 161.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-12 
Deposition Author(s): Seeger, M.A., Schiefner, A., Eicher, T., Verrey, F., Diederichs, K., Pos, K.M.

Revision History  

• Version 1.0: 2006-09-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description