2DRD

Crystal structure of a multidrug transporter reveal a functionally rotating mechanism

PDB DOI: https://doi.org/10.2210/pdb2DRD/pdb

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

Deposited: 2006-06-08 Released: 2006-08-22
Deposition Author(s): Murakami, S., Nakashima, R., Yamashita, E., Matsumoto, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.310
R-Value Work: 0.255
R-Value Observed: 0.257

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1038/nature05076
Primary Citation of 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.

Organizational Affiliation

Department of Cell Membrane Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan. mura@sanken.osaka-u.ac.jp

Macromolecule Content

Total Structure Weight: 343.11 kDa
Atom Count: 23,355
Modelled Residue Count: 3,066
Deposited Residue Count: 3,159
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31224
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MIY Query on MIY Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE C₂₃ H₂₇ N₃ O₇ DYKFCLLONBREIL-KVUCHLLUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.310
R-Value Work: 0.255
R-Value Observed: 0.257
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.801	α = 90
b = 134.466	β = 98.17
c = 162.115	γ = 90

Software Package:

Software Name	Purpose
FFTBIG	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
FFTBIG	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-08-22

Deposition Author(s):

Revision History (Full details and data files)

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, Derived calculations, Structure summary