Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 155.69 kDa 
• Atom Count: 10084 
• Residue Count: 1300 
• Unique protein chains: 2

4KSD

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

• DOI: 10.2210/pdb4KSD/pdb

• Classification: MEMBRANE PROTEIN, TRANSPORT PROTEIN
• Organism(s): Mus musculus, Lama glama
• Expression System: Komagataella pastoris, Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-17 Released: 2013-07-31 
• Deposition Author(s): Ward, A., Szewczyk, P., Grimard, V., Lee, C.-W., Martinez, L., Doshi, R., Caya, A., Villaluz, M., Pardon, E., Cregger, C., Swartz, D.J., Falson, P., Urbatsch, I., Govaerts, C., Steyaert, J., Chang, G.

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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 

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

• PubMed: 23901103 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug resistance protein 1A	A	1284	Mus musculus	Mutation(s): 0  Gene Names: Abcb1a, Abcb4, Mdr1a, Mdr3, Pgy-3, Pgy3 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
R2 protein	B	124	Lama glama	Mutation(s): 0  Gene Names: r2

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 = 87.1	α = 90
b = 102.47	β = 90
c = 312.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-17 
• Released Date: 2013-07-31 
Deposition Author(s): Ward, A., Szewczyk, P., Grimard, V., Lee, C.-W., Martinez, L., Doshi, R., Caya, A., Villaluz, M., Pardon, E., Cregger, C., Swartz, D.J., Falson, P., Urbatsch, I., Govaerts, C., Steyaert, J., Chang, G.

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