8PG0

Human OATP1B3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 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

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 8PHW


Literature

Structure of human drug transporters OATP1B1 and OATP1B3.

Ciuta, A.D.Nosol, K.Kowal, J.Mukherjee, S.Ramirez, A.S.Stieger, B.Kossiakoff, A.A.Locher, K.P.

(2023) Nat Commun 14: 5774-5774

  • DOI: https://doi.org/10.1038/s41467-023-41552-8
  • Primary Citation of Related Structures:  
    8PG0, 8PHW

  • PubMed Abstract: 

    The organic anion transporting polypeptides OATP1B1 and OATP1B3 are membrane proteins that mediate uptake of drugs into the liver for subsequent conjugation and biliary excretion, a key step in drug elimination from the human body. Polymorphic variants of these transporters can cause reduced drug clearance and adverse drug effects such as statin-induced rhabdomyolysis, and co-administration of OATP substrates can lead to damaging drug-drug interaction. Despite their clinical relevance in drug disposition and pharmacokinetics, the structure and mechanism of OATPs are unknown. Here we present cryo-EM structures of human OATP1B1 and OATP1B3 bound to synthetic Fab fragments and in functionally distinct states. A single estrone-3-sulfate molecule is bound in a pocket located in the C-terminal half of OATP1B1. The shape and chemical nature of the pocket rationalize the preference for diverse organic anions and allow in silico docking of statins. The structure of OATP1B3 is determined in a drug-free state but reveals a bicarbonate molecule bound to the conserved signature motif and a histidine residue that is prevalent in OATPs exhibiting pH-dependent activity.


  • Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier organic anion transporter family member 1B3702Homo sapiensMutation(s): 0 
Gene Names: SLCO1B3LST2OATP1B3OATP8SLC21A8
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPD5 (Homo sapiens)
Explore Q9NPD5 
Go to UniProtKB:  Q9NPD5
PHAROS:  Q9NPD5
GTEx:  ENSG00000111700 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NPD5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab19 (heavy chain, variable region)B [auth H]240Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab19 (light chain, variable region)C [auth L]215Homo sapiensMutation(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: 2.97 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 FoundationSwitzerland310030_189111
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117372

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release