8Y6H

P-glycoprotein in complex with UIC2 Fab and triple elacridar molecules in LMNG detergent


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structure of P-glycoprotein bound to triple elacridar inhibitor molecules.

Hamaguchi-Suzuki, N.Adachi, N.Moriya, T.Yasuda, S.Kawasaki, M.Suzuki, K.Ogasawara, S.Anzai, N.Senda, T.Murata, T.

(2024) Biochem Biophys Res Commun 709: 149855-149855

  • DOI: https://doi.org/10.1016/j.bbrc.2024.149855
  • Primary Citation of Related Structures:  
    8Y6H, 8Y6I

  • PubMed Abstract: 

    P-glycoprotein (P-gp) is an ATP-binding cassette transporter known for its roles in expelling xenobiotic compounds from cells and contributing to cellular drug resistance through multidrug efflux. This mechanism is particularly problematic in cancer cells, where it diminishes the therapeutic efficacy of anticancer drugs. P-gp inhibitors, such as elacridar, have been developed to circumvent the decrease in drug efficacy due to P-gp efflux. An earlier study reported the cryo-EM structure of human P-gp-Fab (MRK-16) complex bound by two elacridar molecules, at a resolution of 3.6 Å. In this study, we have obtained a higher resolution (2.5 Å) structure of the P-gp- Fab (UIC2) complex bound by three elacridar molecules. This finding, which exposes a larger space for compound-binding sites than previously acknowledged, has significant implications for the development of more selective inhibitors and enhances our understanding of the compound recognition mechanism of P-gp.


  • Organizational Affiliation

    Department of Pharmacology, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo, Chiba, 260-8670, Japan; Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent translocase ABCB1,mNeonGreen1,534Homo sapiensMutation(s): 0 
Gene Names: ABCB1MDR1PGY1blFP-Y3
EC: 7.6.2.2 (PDB Primary Data), 7.6.2.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P08183 (Homo sapiens)
Explore P08183 
Go to UniProtKB:  P08183
PHAROS:  P08183
GTEx:  ENSG00000085563 
Find proteins for A0A1S4NYF2 (Branchiostoma lanceolatum)
Explore A0A1S4NYF2 
Go to UniProtKB:  A0A1S4NYF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA0A1S4NYF2P08183
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UIC2 Fab light chain220Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
UIC2 Fab heavy chain225Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONcryoSPARC4.2.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101083
Japan Agency for Medical Research and Development (AMED)JapanJP23ama121013
Japan Society for the Promotion of Science (JSPS)Japan18H05425

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release