Cryo-EM structure of the mouse ABCB9 (ADP.BeF3-bound)

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


The lysosomal transporter TAPL has a dual role as peptide translocator and phosphatidylserine floppase.

Park, J.G.Kim, S.Jang, E.Choi, S.H.Han, H.Ju, S.Kim, J.W.Min, D.S.Jin, M.S.

(2022) Nat Commun 13: 5851-5851

  • DOI: https://doi.org/10.1038/s41467-022-33593-2
  • Primary Citation of Related Structures:  
    7V5C, 7V5D, 7VFI

  • PubMed Abstract: 

    TAPL is a lysosomal ATP-binding cassette transporter that translocates a broad spectrum of polypeptides from the cytoplasm into the lysosomal lumen. Here we report that, in addition to its well-known role as a peptide translocator, TAPL exhibits an ATP-dependent phosphatidylserine floppase activity that is the possible cause of its high basal ATPase activity and of the lack of coupling between ATP hydrolysis and peptide efflux. We also present the cryo-EM structures of mouse TAPL complexed with (i) phospholipid, (ii) cholesteryl hemisuccinate (CHS) and 9-mer peptide, and (iii) ADP·BeF 3 . The inward-facing structure reveals that F449 protrudes into the cylindrical transport pathway and divides it into a large hydrophilic central cavity and a sizable hydrophobic upper cavity. In the structure, the peptide binds to TAPL in horizontally-stretched fashion within the central cavity, while lipid molecules plug vertically into the upper cavity. Together, our results suggest that TAPL uses different mechanisms to function as a peptide translocase and a phosphatidylserine floppase.

  • Organizational Affiliation

    School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC-type oligopeptide transporter ABCB9
A, B
762Mus musculusMutation(s): 0 
Gene Names: Abcb9
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9JJ59 (Mus musculus)
Explore Q9JJ59 
Go to UniProtKB:  Q9JJ59
IMPC:  MGI:1861729
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JJ59
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2019M3E5D6063908
National Research Foundation (NRF, Korea)Korea, Republic Of2021M3A9I4022846
National Research Foundation (NRF, Korea)Korea, Republic Of2020R1I1A1A01072077
National Research Foundation (NRF, Korea)Korea, Republic Of2022R1A6A3A13064599

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Data collection