4KSD

Structures of P-glycoprotein reveal its conformational flexibility and an epitope on the nucleotide-binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.323 
  • R-Value Observed: 0.324 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of P-glycoprotein reveal its conformational flexibility and an epitope on the nucleotide-binding domain.

Ward, A.B.Szewczyk, P.Grimard, V.Lee, C.W.Martinez, L.Doshi, R.Caya, A.Villaluz, M.Pardon, E.Cregger, C.Swartz, D.J.Falson, P.G.Urbatsch, I.L.Govaerts, C.Steyaert, J.Chang, G.

(2013) Proc Natl Acad Sci U S A 110: 13386-13391

  • DOI: 10.1073/pnas.1309275110
  • Primary Citation of Related Structures:  
    4KSD, 4KSB, 4KSC

  • PubMed Abstract: 
  • P-glycoprotein (P-gp) is one of the best-known mediators of drug efflux-based multidrug resistance in many cancers. This validated therapeutic target is a prototypic, plasma membrane resident ATP-Binding Cassette transporter that pumps xenobiotic compoun ...

    P-glycoprotein (P-gp) is one of the best-known mediators of drug efflux-based multidrug resistance in many cancers. This validated therapeutic target is a prototypic, plasma membrane resident ATP-Binding Cassette transporter that pumps xenobiotic compounds out of cells. The large, polyspecific drug-binding pocket of P-gp recognizes a variety of structurally unrelated compounds. The transport of these drugs across the membrane is coincident with changes in the size and shape of this pocket during the course of the transport cycle. Here, we present the crystal structures of three inward-facing conformations of mouse P-gp derived from two different crystal forms. One structure has a nanobody bound to the C-terminal side of the first nucleotide-binding domain. This nanobody strongly inhibits the ATP hydrolysis activity of mouse P-gp by hindering the formation of a dimeric complex between the ATP-binding domains, which is essential for nucleotide hydrolysis. Together, these inward-facing conformational snapshots of P-gp demonstrate a range of flexibility exhibited by this transporter, which is likely an essential feature for the binding and transport of large, diverse substrates. The nanobody-bound structure also reveals a unique epitope on P-gp.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Multidrug resistance protein 1A A1284Mus musculusMutation(s): 0 
Gene Names: Abcb1aAbcb4Mdr1aMdr3Pgy-3Pgy3
EC: 3.6.3.44 (PDB Primary Data), 7.6.2.2 (UniProt), 7.6.2.1 (UniProt)
Find proteins for P21447 (Mus musculus)
Explore P21447 
Go to UniProtKB:  P21447
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
R2 protein B124Lama glamaMutation(s): 0 
Gene Names: r2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.323 
  • R-Value Observed: 0.324 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.1α = 90
b = 102.47β = 90
c = 312.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-08-21
    Changes: Database references
  • Version 1.2: 2013-08-28
    Changes: Database references
  • Version 1.3: 2015-09-09
    Changes: Structure summary
  • Version 1.4: 2019-07-17
    Changes: Advisory, Data collection, Refinement description