7S8U | pdb_00007s8u

Cryo-EM structure of a mammalian peptide transporter (PepT1/slc15a1) in nanodisc

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Equus caballus
  • Expression System: Trichoplusia ni
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMPDBTM

  • Deposited: 2021-09-19 Released: 2022-07-20 
  • Deposition Author(s): Shen, J., Zhou, M.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Cancer Prevention and Research Institute of Texas (CPRIT), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Extracellular domain of PepT1 interacts with TM1 to facilitate substrate transport.

Shen, J.Hu, M.Fan, X.Ren, Z.Portioli, C.Yan, X.Rong, M.Zhou, M.

(2022) Structure 30: 1035-1041.e3

  • DOI: https://doi.org/10.1016/j.str.2022.04.011
  • Primary Citation of Related Structures:  
    7S8U

  • PubMed Abstract: 

    Mammalian peptide transporters, PepT1 and PepT2, mediate uptake of small peptides and are essential for their absorption. PepT also mediates absorption of many drugs and prodrugs to enhance their bioavailability. PepT has twelve transmembrane (TM) helices that fold into an N-terminal domain (NTD, TM1-6) and a C-terminal domain (CTD, TM7-12) and has a large extracellular domain (ECD) between TM9-10. It is well recognized that peptide transport requires movements of the NTD and CTD, but the role of the ECD in PepT1 remains unclear. Here we report the structure of horse PepT1 encircled in lipid nanodiscs and captured in the inward-open apo conformation. The structure shows that the ECD bridges the NTD and CTD by interacting with TM1. Deletion of ECD or mutations to the ECD-TM1 interface impairs the transport activity. These results demonstrate an important role of ECD in PepT1 and enhance our understanding of the transport mechanism in PepT1.


  • Organizational Affiliation
    • Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier family 15 member 1707Equus caballusMutation(s): 0 
Gene Names: SLC15A1
Membrane Entity: Yes 
UniProt
Find proteins for F6SG69 (Equus caballus)
Explore F6SG69 
Go to UniProtKB:  F6SG69
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF6SG69
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK122784
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM145416
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL086392
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM098878
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesR1223
National Science Foundation (NSF, United States)United StatesDMR-1420541

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-06-04
    Changes: Data collection