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- EMDB-30165: Cryo-EM structure of a human ATP11C-CDC50A flippase in E1AlF state -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30165 | ||||||||||||
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Title | Cryo-EM structure of a human ATP11C-CDC50A flippase in E1AlF state | ||||||||||||
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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 / early endosome membrane / late endosome membrane / apical plasma membrane / lysosomal membrane / endoplasmic reticulum membrane / Neutrophil degranulation / structural molecule activity / magnesium ion binding / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 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 | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 10.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.9 KB 13.9 KB | Display Display | ![]() |
Images | ![]() | 113.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bssMC ![]() 7bspC ![]() 7bsqC ![]() 7bsuC ![]() 7bsvC ![]() 7bswC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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 : human ATP11C-CDC50A flippase
Entire | Name: human ATP11C-CDC50A flippase |
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Components |
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-Supramolecule #1: human ATP11C-CDC50A flippase
Supramolecule | Name: human ATP11C-CDC50A flippase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Theoretical: 180 KDa |
-Macromolecule #1: ATP11C
Macromolecule | Name: ATP11C / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 124.403617 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: RFCAGEEKRV GTRTVFVGNH PVSETEAYIA QRFCDNRIVS SKYTLWNFLP KNLFEQFRRI ANFYFLIIFL VQVTVDTPTS PVTSGLPLF FVITVTAIKQ GYEDWLRHRA DNEVNKSTVY IIENAKRVRK ESEKIKVGDV VEVQADETFP CDLILLSSCT T DGTCYVTT ...String: RFCAGEEKRV GTRTVFVGNH PVSETEAYIA QRFCDNRIVS SKYTLWNFLP KNLFEQFRRI ANFYFLIIFL VQVTVDTPTS PVTSGLPLF FVITVTAIKQ GYEDWLRHRA DNEVNKSTVY IIENAKRVRK ESEKIKVGDV VEVQADETFP CDLILLSSCT T DGTCYVTT ASLDGESNCK THYAVRDTIA LCTAESIDTL RAAIECEQPQ PDLYKFVGRI NIYSNSLEAV ARSLGPENLL LK GATLKNT EKIYGVAVYT GMETKMALNY QGKSQKRSAV EKSINAFLIV YLFILLTKAA VCTTLKYVWQ STPYNDEPWY NQK TQKERE TLKVLKMFTD FLSFMVLFNF IIPVSMYVTV EMQKFLGSFF ISWDKDFYDE EINEGALVNT SDLNEELGQV DYVF TDKTG TLTENSMEFI ECCIDGHKYK GVTQEVDGLS QTDGTLTYFD KVDKNREELF LRALCLCHTV EIKTNDAVDG ATESA ELTY ISSSPDEIAL VKGAKRYGFT FLGNRNGYMR VENQRKEIEE YELLHTLNFD AVRRRMSVIV KTQEGDILLF CKGADS AVF PRVQNHEIEL TKVHVERNAM DGYRTLCVAF KEIAPDDYER INRQLIEAKM ALQDREEKME KVFDDIETNM NLIGATA VE DKLQDQAAET IEALHAAGLK VWVLTGDKME TAKSTCYACR LFQTNTELLE LTTKTIEESE RKEDRLHELL IEYRKKLL H EFPKSTRSFK KAWTEHQEYG LIIDGSTLSL ILNSSQDSSS NNYKSIFLQI CMKCTAVLCC RMAPLQKAQI VRMVKNLKG SPITLSIGDG ANDVSMILES HVGIGIKGKE GRQAARNSDY SVPKFKHLKK LLLAHGHLYY VRIAHLVQYF FYKNLCFILP QFLYQFFCG FSQQPLYDAA YLTMYNICFT SLPILAYSLL EQHINIDTLT SDPRLYMKIS GNAMLQLGPF LYWTFLAAFE G TVFFFGTY FLFQTASLEE NGKVYGNWTF GTIVFTVLVF TVTLKLALDT RFWTWINHFV IWGSLAFYVF FSFFWGGIIW PF LKQQRMY FVFAQMLSSV STWLAIILLI FISLFPEILL IVLKNVR |
-Macromolecule #2: CDC50A
Macromolecule | Name: CDC50A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 40.900801 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MAMNYNAKDE VDGGPPCAPG GTAKTRRPDN TAFKQQRLPA WQPILTAGTV LPIFFIIGLI FIPIGIGIFV TSNNIREIEI DYTGTEPSS PCNKCLSPDV TPCFCTINFT LEKSFEGNVF MYYGLSNFYQ NHRRYVKSRD DSQLNGDSSA LLNPSKECEP Y RRNEDKPI ...String: MAMNYNAKDE VDGGPPCAPG GTAKTRRPDN TAFKQQRLPA WQPILTAGTV LPIFFIIGLI FIPIGIGIFV TSNNIREIEI DYTGTEPSS PCNKCLSPDV TPCFCTINFT LEKSFEGNVF MYYGLSNFYQ NHRRYVKSRD DSQLNGDSSA LLNPSKECEP Y RRNEDKPI APCGAIMNSM FNDTLELFLI GQDSYPIPIA LKKKGIAWWT DKNVKFRNPP GGDNLEERFK GTTKPVNWLK PV YMLDSDP DNNGFINEDF IVWMRTAALP TFRKLYRLIE RKSDLHPTLP AGRYWLNVTY NYPVHYFDGR KRMILSTISW MGG KNPFLG IAYIAVGSIS FLLGVVLLVI NHKYRNSSNT ADITI |
-Macromolecule #3: TETRAFLUOROALUMINATE ION
Macromolecule | Name: TETRAFLUOROALUMINATE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ALF |
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Molecular weight | Theoretical: 102.975 Da |
Chemical component information | ![]() ChemComp-ALF: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #6: alpha-D-mannopyranose
Macromolecule | Name: alpha-D-mannopyranose / type: ligand / ID: 6 / Number of copies: 1 / Formula: MAN |
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Molecular weight | Theoretical: 180.156 Da |
Chemical component information | ![]() ChemComp-MAN: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 8 mg/mL |
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Buffer | pH: 6.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 500000 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-7bss: |