8PMD | pdb_00008pmd

Nucleotide-bound BSEP in nanodiscs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural basis of bile salt extrusion and small-molecule inhibition in human BSEP.

Liu, H.Irobalieva, R.N.Kowal, J.Ni, D.Nosol, K.Bang-Sorensen, R.Lancien, L.Stahlberg, H.Stieger, B.Locher, K.P.

(2023) Nat Commun 14: 7296-7296

  • DOI: https://doi.org/10.1038/s41467-023-43109-1
  • Primary Citation Related Structures: 
    8PM6, 8PMD, 8PMJ

  • PubMed Abstract: 

    BSEP (ABCB11) is an ATP-binding cassette transporter that is expressed in hepatocytes and extrudes bile salts into the canaliculi of the liver. BSEP dysfunction, caused by mutations or induced by drugs, is frequently associated with severe cholestatic liver disease. We report the cryo-EM structure of glibenclamide-bound human BSEP in nanodiscs, revealing the basis of small-molecule inhibition. Glibenclamide binds the apex of a central binding pocket between the transmembrane domains, preventing BSEP from undergoing conformational changes, and thus rationalizing the reduced uptake of bile salts. We further report two high-resolution structures of BSEP trapped in distinct nucleotide-bound states by using a catalytically inactivated BSEP variant (BSEP E1244Q ) to visualize a pre-hydrolysis state, and wild-type BSEP trapped by vanadate to visualize a post-hydrolysis state. Our studies provide structural and functional insight into the mechanism of bile salt extrusion and into small-molecule inhibition of BSEP, which may rationalize drug-induced liver toxicity.


  • Organizational Affiliation
    • Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 147.62 kDa 
  • Atom Count: 8,844 
  • Modeled Residue Count: 1,129 
  • Deposited Residue Count: 1,321 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bile salt export pump1,321Homo sapiensMutation(s): 0 
Gene Names: ABCB11BSEP
EC: 7.6.2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O95342 (Homo sapiens)
Explore O95342 
Go to UniProtKB:  O95342
PHAROS:  O95342
GTEx:  ENSG00000073734 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95342
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland189111
Swiss National Science FoundationSwitzerland206089
Swiss National Science FoundationSwitzerland185544

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Data collection, Structure summary