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- PDB-7bsu: Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdSer-bou... -
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Basic information
Entry | Database: PDB / ID: 7bsu | ||||||||||||
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Title | Cryo-EM structure of a human ATP11C-CDC50A flippase in PtdSer-bound E2BeF state | ||||||||||||
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![]() | MEMBRANE PROTEIN / Flippase / P-type ATPase / P4-ATPase / Phospholipid | ||||||||||||
Function / homology | ![]() positive regulation of phospholipid translocation / aminophospholipid flippase activity / aminophospholipid transport / phosphatidylserine flippase activity / protein localization to endosome / phospholipid-translocating ATPase complex / ATPase-coupled intramembrane lipid transporter activity / phosphatidylserine floppase activity / positive regulation of protein exit from endoplasmic reticulum / phosphatidylethanolamine flippase activity ...positive regulation of phospholipid translocation / aminophospholipid flippase activity / aminophospholipid transport / phosphatidylserine flippase activity / protein localization to endosome / phospholipid-translocating ATPase complex / ATPase-coupled intramembrane lipid transporter activity / phosphatidylserine floppase activity / positive regulation of protein exit from endoplasmic reticulum / phosphatidylethanolamine flippase activity / xenobiotic transmembrane transport / P-type phospholipid transporter / phospholipid translocation / transport vesicle membrane / azurophil granule membrane / Ion transport by P-type ATPases / specific granule membrane / monoatomic ion transmembrane transport / recycling endosome / positive regulation of neuron projection development / recycling endosome membrane / late endosome membrane / early endosome membrane / apical plasma membrane / lysosomal membrane / Neutrophil degranulation / endoplasmic reticulum membrane / structural molecule activity / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
![]() | Abe, K. / Nishizawa, T. / Nakanishi, H. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Transport Cycle of Plasma Membrane Flippase ATP11C by Cryo-EM. Authors: Hanayo Nakanishi / Tomohiro Nishizawa / Katsumori Segawa / Osamu Nureki / Yoshinori Fujiyoshi / Shigekazu Nagata / Kazuhiro Abe / ![]() Abstract: ATP11C, 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. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 225.4 KB | Display | ![]() |
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PDB format | ![]() | 175.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 30167MC ![]() 7bspC ![]() 7bsqC ![]() 7bssC ![]() 7bsvC ![]() 7bswC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 2 molecules AC
#1: Protein | Mass: 124468.617 Da / Num. of mol.: 1 / Mutation: Delete 7 a.a. at N-term, and 38 a.a. at C-term Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 40900.801 Da / Num. of mol.: 1 / Mutation: A175M, N190Q, S292W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 2 types, 5 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/AH2.gif)
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#5: Sugar | ChemComp-NAG / #6: Sugar | ChemComp-AH2 / | |
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-Non-polymers , 2 types, 2 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/P5S.gif)
![](data/chem/img/P5S.gif)
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-P5S / |
-Details
Has ligand of interest | Y |
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Sequence details | NCBI Reference Sequence accession IDs are NCBI XM_005262405.1 for ATP11C and NP_001340741.2 for CDC50A. |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: human ATP11C-CDC50A flippase / Type: COMPLEX / Entity ID: #2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.18 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 6.5 |
Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 298 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 64 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 500000 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.15 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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