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TitleTransport Cycle of Plasma Membrane Flippase ATP11C by Cryo-EM.
Journal, issue, pagesCell Rep, Vol. 32, Issue 13, Page 108208, Year 2020
Publish dateSep 29, 2020
AuthorsHanayo Nakanishi / Tomohiro Nishizawa / Katsumori Segawa / Osamu Nureki / Yoshinori Fujiyoshi / Shigekazu Nagata / Kazuhiro Abe /
PubMed AbstractATP11C, a plasma membrane phospholipid flippase, maintains the asymmetric distribution of phosphatidylserine accumulated in the inner leaflet. Caspase-dependent inactivation of ATP11C is essential ...ATP11C, a plasma membrane phospholipid flippase, maintains the asymmetric distribution of phosphatidylserine accumulated in the inner leaflet. Caspase-dependent inactivation of ATP11C is essential for an apoptotic "eat me" signal, phosphatidylserine exposure, which prompts phagocytes to engulf cells. We show six cryo-EM structures of ATP11C at 3.0-4.0 Å resolution in five different states of the transport cycle. A structural comparison reveals phosphorylation-driven domain movements coupled with phospholipid binding. Three structures of phospholipid-bound states visualize phospholipid translocation accompanied by the rearrangement of transmembrane helices and an unwound portion at the occlusion site, and thus they detail the basis for head group recognition and the locality of the protein-bound acyl chains in transmembrane grooves. Invariant Lys880 and the surrounding hydrogen-bond network serve as a pivot point for helix bending and precise P domain inclination, which is crucial for dephosphorylation. The structures detail key features of phospholipid translocation by ATP11C, and a common basic mechanism for flippases is emerging.
External linksCell Rep / PubMed:32997992
MethodsEM (single particle)
Resolution3.0 - 4.0 Å
Structure data

30163

7bsp

EMDB-30163, PDB-7bsp:
Cryo-EM structure of a human ATP11C-CDC50A flippase in E1-AMPPCP state
Method: EM (single particle) / Resolution: 4.0 Å

30164

7bsq

EMDB-30164, PDB-7bsq:
Cryo-EM structure of a human ATP11C-CDC50A flippase in E1AlF-ADP state
Method: EM (single particle) / Resolution: 3.2 Å

30165

7bss

EMDB-30165, PDB-7bss:
Cryo-EM structure of a human ATP11C-CDC50A flippase in E1AlF state
Method: EM (single particle) / Resolution: 3.3 Å

30167

7bsu

EMDB-30167, PDB-7bsu:
Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdSer-bound E2BeF state
Method: EM (single particle) / Resolution: 3.2 Å

30168

7bsv

EMDB-30168, PDB-7bsv:
Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdSer-occluded E2-AlF state
Method: EM (single particle) / Resolution: 3.0 Å

30169

7bsw

EMDB-30169, PDB-7bsw:
Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdEtn-occluded E2-AlF state
Method: EM (single particle) / Resolution: 3.9 Å

Chemicals

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

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

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

ChemComp-MG:
Unknown entry

ChemComp-MAN:
alpha-D-mannopyranose / Mannose

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / Phosphatidylserine

ChemComp-AH2:
1-deoxy-alpha-D-mannopyranose

ChemComp-HOH:
WATER / Water

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM / Discrete optimized protein energy

Source
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / Flippase / P-type ATPase / P4-ATPase / Phospholipid

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