8OP3

Cryo-EM structure of P5A-ATPase CtSpf1 (E1 state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 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

The structure and function of P5A-ATPases.

Li, P.Bagenholm, V.Hagglund, P.Lindkvist-Petersson, K.Wang, K.Gourdon, P.

(2024) Nat Commun 15: 9605-9605

  • DOI: https://doi.org/10.1038/s41467-024-53757-6
  • Primary Citation of Related Structures:  
    8OP3, 8OP4, 8OP5, 8OP6, 8OP7, 8OP8

  • PubMed Abstract: 

    Endoplasmic reticulum (ER) membrane resident P5A-ATPases broadly affect protein biogenesis and quality control, and yet their molecular function remains debated. Here, we report cryo-EM structures of a P5A-ATPase, CtSpf1, covering multiple transport intermediates of the E1 → E1-ATP → E1P-ADP → E1P → E2P → E2.P i  → E2 → E1 cycle. In the E2P and E2.P i states a cleft spans the entire membrane, holding a polypeptide cargo molecule. The cargo includes an ER luminal extension, pinpointed as the C-terminus in the E2.P i state, which reenters the membrane in E2P. The E1 structure harbors a cytosol-facing cavity that is blocked by an insertion we refer to as the Plug-domain. The Plug-domain is nestled to key ATPase features and is displaced in the E1P-ADP and E1P states. Collectively, our findings are compatible with a broad range of proteins as cargo, with the P5A-ATPases serving a role in membrane removal of helices, although insertion/secretion cannot be excluded, as well as with a mechanistic role of the Plug-domain.


  • Organizational Affiliation

    Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84, Lund, Sweden. ping.li@med.lu.se.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cation-transporting ATPase-like protein1,328Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0032200
Membrane Entity: Yes 
UniProt
Find proteins for G0S4Z4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S4Z4 
Go to UniProtKB:  G0S4Z4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S4Z4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden2020.0194
Swedish Research CouncilSweden2022-01315
The Crafoord FoundationSweden20200739
LundbeckfondenDenmarkR346-2020-2019

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references