8PMJ

Vanadate-trapped BSEP in nanodiscs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 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

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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
G [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
VO4 (Subject of Investigation/LOI)
Query on VO4

Download Ideal Coordinates CCD File 
H [auth A]VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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: 2023-11-29
    Type: Initial release