9JBX | pdb_00009jbx

P5A-ATPase ATP13A1 in E1P state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 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


Literature

ATP13A1 engages SEC61 to facilitate substrate-specific translocation.

Yang, X.Li, Y.Yang, C.Li, T.Fang, Z.Feng, Z.Liao, J.Zou, Y.

(2025) Sci Adv 11: eadt1346-eadt1346

  • DOI: https://doi.org/10.1126/sciadv.adt1346
  • Primary Citation of Related Structures:  
    9JBM, 9JBR, 9JBX, 9JBZ

  • PubMed Abstract: 

    The accurate targeting of proteins to their designated cellular compartments is essential for maintaining proper cellular architecture and function. However, interpreting and sorting the highly variable targeting sequences in secreted and membrane proteins present a substantial challenge for achieving precise localization within the secretory pathway. In this study, we demonstrate that atypical signal sequences, characterized by high hydrophobicity and/or the absence of characteristic charges, are recognized by the signal recognition particle and targeted to the endoplasmic reticulum in a reverse orientation. These misoriented signal sequences are subsequently dislocated by the P5A-ATPase ATP13A1 and delivered to SEC61 for further translocation. Using cryo-electron microscopy, we determined the structures of human ATP13A1 in multiple conformations (3.40- to 3.87-angstrom resolution), revealing key residues within its substrate-binding pocket that engage signal sequences through polar interactions. Collectively, our findings elucidate a comprehensive, substrate-specific translocation pathway that ensures both high efficiency and fidelity in protein subcellular localization.


  • Organizational Affiliation

    School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoplasmic reticulum transmembrane helix translocase1,079Homo sapiensMutation(s): 0 
Gene Names: ATP13A1ATP13AKIAA1825CGI-152
EC: 7.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HD20 (Homo sapiens)
Explore Q9HD20 
Go to UniProtKB:  Q9HD20
PHAROS:  Q9HD20
GTEx:  ENSG00000105726 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HD20
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Data collection, Database references