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Structure paper

TitleThe structure and function of P5A-ATPases.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 9605, Year 2024
Publish dateNov 6, 2024
AuthorsPing Li / Viktoria Bågenholm / Per Hägglund / Karin Lindkvist-Petersson / Kaituo Wang / Pontus Gourdon /
PubMed AbstractEndoplasmic 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 ...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 → E2 → E1 cycle. In the E2P and E2.P 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 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.
External linksNat Commun / PubMed:39505844 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 3.79 Å
Structure data

17039

8op3

EMDB-17039, PDB-8op3:
Cryo-EM structure of P5A-ATPase CtSpf1 (E1 state)
Method: EM (single particle) / Resolution: 3.41 Å

17040

8op4

EMDB-17040, PDB-8op4:
Cryo-EM structure of P5A-ATPase CtSpf1 (E1-ATP state)
Method: EM (single particle) / Resolution: 3.2 Å

17041

8op5

EMDB-17041, PDB-8op5:
Cryo-EM structure of P5A-ATPase CtSpf1 (E1P-ADP state with membranous-feature bound)
Method: EM (single particle) / Resolution: 3.47 Å

17042

8op6

EMDB-17042, PDB-8op6:
Cryo-EM structure of P5A-ATPase CtSpf1 (E1P state with cytosolic-feature bound)
Method: EM (single particle) / Resolution: 3.79 Å

17043

8op7

EMDB-17043, PDB-8op7:
Cryo-EM structure of P5A-ATPase CtSpf1 ( E2P state with endogenous cargo bound)
Method: EM (single particle) / Resolution: 3.5 Å

17044

8op8

EMDB-17044, PDB-8op8:
Cryo-EM structure of P5A-ATPase CtSpf1 (E2.Pi state with endogenous helix cargo bound)
Method: EM (single particle) / Resolution: 3.48 Å

Chemicals

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

ChemComp-HOH:
WATER

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-CA:
Unknown entry

Source
  • thermochaetoides thermophila (fungus)
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsMEMBRANE PROTEIN / translocase

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