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Structure paper

TitleConformational changes of a phosphatidylcholine flippase in lipid membranes.
Journal, issue, pagesCell Rep, Vol. 38, Issue 11, Page 110518, Year 2022
Publish dateMar 15, 2022
AuthorsJinkun Xu / Yilin He / Xiaofei Wu / Long Li /
PubMed AbstractType 4 P-type ATPases (P4-ATPases) actively and selectively translocate phospholipids across membrane bilayers. Driven by ATP hydrolysis, P4-ATPases undergo conformational changes during lipid ...Type 4 P-type ATPases (P4-ATPases) actively and selectively translocate phospholipids across membrane bilayers. Driven by ATP hydrolysis, P4-ATPases undergo conformational changes during lipid flipping. It is unclear how the active flipping states of P4-ATPases are regulated in the lipid membranes, especially for phosphatidylcholine (PC)-flipping P4-ATPases whose substrate, PC, is a substantial component of membranes. Here, we report the cryoelectron microscopy structures of a yeast PC-flipping P4-ATPase, Dnf1, in lipid environments. In native yeast lipids, Dnf1 adopts a conformation in which the lipid flipping pathway is disrupted. Only when the lipid composition is changed can Dnf1 be captured in the active conformations that enable lipid flipping. These results suggest that, in the native membrane, Dnf1 may stay in an idle conformation that is unable to support the trans-membrane movement of lipids. Dnf1 may have altered conformational preferences in membranes with different lipid compositions.
External linksCell Rep / PubMed:35294892
MethodsEM (single particle)
Resolution2.8 - 3.81 Å
Structure data

30829

7drx

EMDB-30829, PDB-7drx:
Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in 90PS with beryllium fluoride (E2P state)
Method: EM (single particle) / Resolution: 2.9 Å

30833

7dsh

EMDB-30833, PDB-7dsh:
Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in 90PS with AMPPCP (E1-ATP state)
Method: EM (single particle) / Resolution: 3.67 Å

30834

7dsi

EMDB-30834, PDB-7dsi:
Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in yeast lipids with AMPPCP ( resting state )
Method: EM (single particle) / Resolution: 3.21 Å

31487

7f7f

EMDB-31487, PDB-7f7f:
Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in yeast lipids with beryllium fluoride (resting state)
Method: EM (single particle) / Resolution: 3.81 Å

32512

7whv

EMDB-32512, PDB-7whv:
Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in detergent with beryllium fluoride (E2P state)
Method: EM (single particle) / Resolution: 2.8 Å

32513

7whw

EMDB-32513, PDB-7whw:
Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in detergent with AMPPCP (E1-ATP state)
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-6PL:
(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / phospholipid*YM

ChemComp-ACP:
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / AMP-PCP, energy-carrying molecule analogue*YM

Source
  • saccharomyces cerevisiae s288c (yeast)
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsLIPID TRANSPORT / P4-ATPases

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