7FJP

Cryo EM structure of lysosomal ATPase

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2021-08-04 Released: 2023-03-08 
  • Deposition Author(s): Zhang, S.S.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

Cryo-EM structures and transport mechanism of human P5B type ATPase ATP13A2.

Chen, X.Zhou, M.Zhang, S.Yin, J.Zhang, P.Xuan, X.Wang, P.Liu, Z.Zhou, B.Yang, M.

(2021) Cell Discov 7: 106-106

  • DOI: https://doi.org/10.1038/s41421-021-00334-6
  • Primary Citation of Related Structures:  
    7FJM, 7FJP, 7FJQ

  • PubMed Abstract: 

    Polyamines are important polycations that play critical roles in mammalian cells. ATP13A2 belongs to the orphan P5B adenosine triphosphatases (ATPase) family and has been established as a lysosomal polyamine exporter to maintain the normal function of lysosomes and mitochondria. Previous studies have reported that several human neurodegenerative disorders are related to mutations in the ATP13A2 gene. However, the transport mechanism of ATP13A2 in the lysosome remains unclear. Here, we report the cryo-electron microscopy (cryo-EM) structures of three distinct intermediates of the human ATP13A2, revealing key insights into the spermine (SPM) transport cycle in the lysosome. The transmembrane domain serves as a substrate binding site and the C-terminal domain is essential for protein stability and may play a regulatory role. These findings advance our understanding of the polyamine transport mechanism, the lipid-associated regulation, and the disease-associated mutants of ATP13A2.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyamine-transporting ATPase 13A2A [auth B]1,148Homo sapiensMutation(s): 0 
Gene Names: ATP13A2
EC: 7.6.2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQ11 (Homo sapiens)
Explore Q9NQ11 
Go to UniProtKB:  Q9NQ11
PHAROS:  Q9NQ11
GTEx:  ENSG00000159363 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NQ11
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2023-03-08 
  • Deposition Author(s): Zhang, S.S.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21532004, 31570733

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release