7OP3 | pdb_00007op3

Cryo-EM structure of P5B-ATPase E2PiSPM

• PDB DOI: https://doi.org/10.2210/pdb7OP3/pdb
• EM Map EMD-13012: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Thermochaetoides thermophila DSM 1495
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2021-05-28 Released: 2021-06-30 
• Deposition Author(s): Li, P., Gronberg, C., Wang, K.T., Salustros, N., Gourdon, P.E.
• Funding Organization(s): Knut and Alice Wallenberg Foundation, Lundbeckfonden

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structure and transport mechanism of P5B-ATPases.

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

(2021) Nat Commun 12: 3973-3973

• PubMed: 34172751 
• DOI: https://doi.org/10.1038/s41467-021-24148-y
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Experimental Medical Science, Lund University, Lund, Sweden.
Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark.
Department of Experimental Medical Science, Lund University, Lund, Sweden. [e-mail].
Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 156.34 kDa 
• Atom Count: 8,772 
• Modeled Residue Count: 1,100 
• Deposited Residue Count: 1,394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation-transporting ATPase	A	1,394	Thermochaetoides thermophila DSM 1495	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM (Subject of Investigation/LOI)	B [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Li, P., Gronberg, C., Wang, K.T., Salustros, N., Gourdon, P.E.

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Funding Organization	Location	Grant Number
Knut and Alice Wallenberg Foundation	Sweden	2020.0914, 2015.0313
Lundbeckfonden	Sweden	R313-2019-774, R218-2016-1548, R133-A12689

Revision History  

• Version 1.0: 2021-06-30
  Type: Initial release
  
• Version 1.1: 2021-07-07
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Refinement description