2DHH | pdb_00002dhh

Crystal structure of a multidrug transporter reveal a functionally rotating mechanism

• PDB DOI: https://doi.org/10.2210/pdb2DHH/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli K-12
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2006-03-23 Released: 2006-08-22 
• Deposition Author(s): Murakami, S., Nakashima, R., Yamashita, E., Matsumoto, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.307 (Depositor), 0.307 (DCC) 
• R-Value Work: 
  0.268 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.270 (Depositor) 

Literature

Crystal structures of a multidrug transporter reveal a functionally rotating mechanism

Murakami, S., Nakashima, R., Yamashita, E., Matsumoto, T., Yamaguchi, A.

(2006) Nature 443: 173-179

• PubMed: 16915237 
• DOI: https://doi.org/10.1038/nature05076
• Primary Citation Related Structures: 
  2DHH, 2DR6, 2DRD


• PubMed Abstract: 
  

  AcrB is a principal multidrug efflux transporter in Escherichia coli that cooperates with an outer-membrane channel, TolC, and a membrane-fusion protein, AcrA. Here we describe crystal structures of AcrB with and without substrates. The AcrB-drug complex consists of three protomers, each of which has a different conformation corresponding to one of the three functional states of the transport cycle. Bound substrate was found in the periplasmic domain of one of the three protomers. The voluminous binding pocket is aromatic and allows multi-site binding. The structures indicate that drugs are exported by a three-step functionally rotating mechanism in which substrates undergo ordered binding change.

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Organizational Affiliation: 
• Department of Cell Membrane Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan. [e-mail]

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: 342.65 kDa 
• Atom Count: 23,378 
• Modeled Residue Count: 3,066 
• Deposited Residue Count: 3,159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACRB	A, B, C	1,053	Escherichia coli	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224  Go to UniProtKB:  P31224

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.307 (Depositor), 0.307 (DCC) 
• R-Value Work:  0.268 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.270 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.87	α = 90
b = 134.418	β = 97.71
c = 163.192	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-22 
Deposition Author(s): Murakami, S., Nakashima, R., Yamashita, E., Matsumoto, T.

Revision History  

• Version 1.0: 2006-08-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references