7OP1

Cryo-EM structure of P5B-ATPase E2PiAlF/SPM


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

Structure and transport mechanism of P5B-ATPases.

Li, P.Wang, K.Salustros, N.Gronberg, C.Gourdon, P.

(2021) Nat Commun 12: 3973-3973

  • DOI: 10.1038/s41467-021-24148-y
  • Primary Citation of Related Structures:  
    7OP1, 7OP3, 7OP5, 7OP8

  • PubMed Abstract: 
  • In human cells, P5B-ATPases execute the active export of physiologically important polyamines such as spermine from lysosomes to the cytosol, a function linked to a palette of disorders. Yet, the overall shape of P5B-ATPases and the mechanisms of polyamine recognition, uptake and transport remain elusive ...

    In human cells, P5B-ATPases execute the active export of physiologically important polyamines such as spermine from lysosomes to the cytosol, a function linked to a palette of disorders. Yet, the overall shape of P5B-ATPases and the mechanisms of polyamine recognition, uptake and transport remain elusive. Here we describe a series of cryo-electron microscopy structures of a yeast homolog of human ATP13A2-5, Ypk9, determined at resolutions reaching 3.4 Å, and depicting three separate transport cycle intermediates, including spermine-bound conformations. Surprisingly, in the absence of cargo, Ypk9 rests in a phosphorylated conformation auto-inhibited by the N-terminus. Spermine uptake is accomplished through an electronegative cleft lined by transmembrane segments 2, 4 and 6. Despite the dramatically different nature of the transported cargo, these findings pinpoint shared principles of transport and regulation among the evolutionary related P4-, P5A- and P5B-ATPases. The data also provide a framework for analysis of associated maladies, such as Parkinson's disease.


    Organizational Affiliation

    Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark. pontus.gourdon@med.lu.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cation-transporting ATPaseA1,393Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0028100
EC: 7.2.2
Membrane Entity: Yes 
UniProt
Find proteins for G0S7G9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S7G9 
Go to UniProtKB:  G0S7G9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S7G9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM (Subject of Investigation/LOI)
Query on SPM

Download Ideal Coordinates CCD File 
D [auth A]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
ALF (Subject of Investigation/LOI)
Query on ALF

Download Ideal Coordinates CCD File 
C [auth A]TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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, 2015.0131
LundbeckfondenDenmarkR313-2019-774, R218-2016-1548, R133-A12689
Danish Council for Independent ResearchDenmark9039-00273, 6108-00479
Swedish Research CouncilSweden2016-04474

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Database references, Structure summary
  • Version 1.2: 2021-09-01
    Changes: Database references, Structure summary