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- EMDB-9931: Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1 ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9931 | ||||||
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Title | Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1 state class1) | ||||||
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![]() | ATP8A1-CDC50a: Phospholipid-transporting ATPase / Cell cycle control protein 50A / (ligand ![]() | ||||||
Function / homology | ![]() ATPase-coupled intramembrane lipid transporter activity / aminophospholipid flippase activity / aminophospholipid transport / positive regulation of protein exit from endoplasmic reticulum / protein localization to endosome / P-type phospholipid transporter / phospholipid transport / phospholipid translocation / azurophil granule membrane / drug transmembrane transport ...ATPase-coupled intramembrane lipid transporter activity / aminophospholipid flippase activity / aminophospholipid transport / positive regulation of protein exit from endoplasmic reticulum / protein localization to endosome / P-type phospholipid transporter / phospholipid transport / phospholipid translocation / azurophil granule membrane / drug transmembrane transport / transport vesicle membrane / specific granule membrane / positive regulation of neuron projection development / apical plasma membrane / neutrophil degranulation / ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hiraizumi M / Yamashita K / Nishizawa T / Nureki O | ||||||
![]() | Journal: Science / Year: 2019 Title: Cryo-EM structures capture the transport cycle of the P4-ATPase flippase. Authors: Masahiro Hiraizumi / Keitaro Yamashita / Tomohiro Nishizawa / Osamu Nureki / ![]() Abstract: In eukaryotic membranes, type IV P-type adenosine triphosphatases (P4-ATPases) mediate the translocation of phospholipids from the outer to the inner leaflet and maintain lipid asymmetry, which is ...In eukaryotic membranes, type IV P-type adenosine triphosphatases (P4-ATPases) mediate the translocation of phospholipids from the outer to the inner leaflet and maintain lipid asymmetry, which is critical for membrane trafficking and signaling pathways. Here, we report the cryo-electron microscopy structures of six distinct intermediates of the human ATP8A1-CDC50a heterocomplex at resolutions of 2.6 to 3.3 angstroms, elucidating the lipid translocation cycle of this P4-ATPase. ATP-dependent phosphorylation induces a large rotational movement of the actuator domain around the phosphorylation site in the phosphorylation domain, accompanied by lateral shifts of the first and second transmembrane helices, thereby allowing phosphatidylserine binding. The phospholipid head group passes through the hydrophilic cleft, while the acyl chain is exposed toward the lipid environment. These findings advance our understanding of the flippase mechanism and the disease-associated mutants of P4-ATPases. | ||||||
Validation Report | PDB-ID: 6k7g![]() ![]() ![]() | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
FSC (resolution estimation) |
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Header (meta data in XML format) |
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Images |
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Others |
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Archive directory |
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Links
EMDB pages | ![]() ![]() |
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EM raw data | ![]() Data #1: Unaligned movies for E2P class 1,2,3 [micrographs - multiframe] Data #2: Unaligned movies for E2Pi-PL and E1P [micrographs - multiframe] Data #3: Unaligned movies for E1P-ADP [micrographs - multiframe] Data #4: Unaligned movies for E1 class1,2,3 [micrographs - multiframe] Data #5: Unaligned movies for E1-ATP class 1,2,3 [micrographs - multiframe]) |
-Related structure data
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire ATP8A1-CDC50a
+Component #1: protein, ATP8A1-CDC50a
+Component #2: protein, Phospholipid-transporting ATPase
+Component #3: protein, Cell cycle control protein 50A
+Component #4: ligand, N-ACETYL-D-GLUCOSAMINE
+Component #5: ligand, ALPHA-D-MANNOSE
+Component #6: ligand, CHOLESTEROL HEMISUCCINATE
-Experimental details
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Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
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Sample solution | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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![]() | Microscope: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: OTHER |
Camera | Detector: OTHER |
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Image processing
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF |
FSC plot (resolution estimation)![]() | ![]() |
-Atomic model buiding
Output model |
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