4M2T: Corrected Structure Of Mouse P-glycoprotein Bound To Qz59-sss

Citation:
Abstract
The recently determined C. elegans P-glycoprotein (Pgp) structure revealed significant deviations compared to the original mouse Pgp structure, which suggested possible misinterpretations in the latter model. To address this concern, we generated an experimental electron density map from single-wavelength anomalous dispersion phasing of an original mouse Pgp dataset to 3.8 A resolution. The map exhibited significantly more detail compared to the original MAD map and revealed several regions of the structure that required de novo model building. The improved drug-free structure was refined to 3.8 A resolution with a 9.4 and 8.1% decrease in Rwork and Rfree , respectively, (Rwork = 21.2%, Rfree = 26.6%) and a significant improvement in protein geometry. The improved mouse Pgp model contains approximately 95% of residues in the favorable Ramachandran region compared to only 57% for the original model. The registry of six transmembrane helices was corrected, revealing amino acid residues involved in drug binding that were previously unrecognized. Registry shifts (rotations and translations) for three transmembrane (TM)4 and TM5 and the addition of three N-terminal residues were necessary, and were validated with new mercury labeling and anomalous Fourier density. The corrected position of TM4, which forms the frame of a portal for drug entry, had backbone atoms shifted >6 A from their original positions. The drug translocation pathway of mouse Pgp is 96% identical to human Pgp and is enriched in aromatic residues that likely play a collective role in allowing a high degree of polyspecific substrate recognition.
PDB ID: 4M2TDownload
MMDB ID: 115130
PDB Deposition Date: 2013/8/5
Updated in MMDB: 2013/11
Experimental Method:
x-ray diffraction
Resolution: 4.35  Å
Source Organism:
Similar Structures:
Biological Unit for 4M2T: monomeric; determined by author and by software (PISA)
Molecular Components in 4M2T
Label Count Molecule
Protein (1 molecule)
1
Multidrug Resistance Protein 1A(Gene symbol: Abcb1a)
Molecule annotation
Chemicals (2 molecules)
1
2
* Click molecule labels to explore molecular sequence information.

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