[English] 日本語
![](img/lk-miru.gif)
- EMDB-9939: Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2P... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-9939 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2P state class2) | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
Function / homology | ![]() aminophospholipid translocation / positive regulation of phospholipid translocation / aminophospholipid flippase activity / aminophospholipid transport / chromaffin granule membrane / phosphatidylserine flippase activity / protein localization to endosome / phospholipid-translocating ATPase complex / ATPase-coupled intramembrane lipid transporter activity / phosphatidylserine floppase activity ...aminophospholipid translocation / positive regulation of phospholipid translocation / aminophospholipid flippase activity / aminophospholipid transport / chromaffin granule membrane / 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 / xenobiotic transmembrane transport / ATPase-coupled monoatomic cation transmembrane transporter activity / P-type phospholipid transporter / phospholipid translocation / transport vesicle membrane / azurophil granule membrane / organelle membrane / Ion transport by P-type ATPases / transport across blood-brain barrier / endomembrane system / specific granule membrane / monoatomic ion transmembrane transport / learning / trans-Golgi network / synaptic vesicle membrane / positive regulation of neuron projection development / early endosome membrane / late endosome membrane / cytoplasmic vesicle / positive regulation of cell migration / apical plasma membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / structural molecule activity / magnesium ion binding / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.83 Å | |||||||||
![]() | Hiraizumi M / Yamashita K / Nishizawa T / Nureki O | |||||||||
![]() | ![]() 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. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 9.5 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 16.8 KB 16.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.3 KB | Display | ![]() |
Images | ![]() | 54.5 KB | ||
Masks | ![]() | 67 MB | ![]() | |
Others | ![]() ![]() | 52.1 MB 52.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6k7lMC ![]() 9931C ![]() 9932C ![]() 9933C ![]() 9934C ![]() 9935C ![]() 9936C ![]() 9937C ![]() 9938C ![]() 9940C ![]() 9941C ![]() 9942C ![]() 6k7gC ![]() 6k7hC ![]() 6k7iC ![]() 6k7jC ![]() 6k7kC ![]() 6k7mC ![]() 6k7nC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | |
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]) |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_9939_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_9939_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : ATP8A1-CDC50a
Entire | Name: ATP8A1-CDC50a |
---|---|
Components |
|
-Supramolecule #1: ATP8A1-CDC50a
Supramolecule | Name: ATP8A1-CDC50a / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Phospholipid-transporting ATPase
Macromolecule | Name: Phospholipid-transporting ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type phospholipid transporter |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 130.537852 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GSREFMPTMR RTVSEIRSRA EGYEKTDDVS EKTSLADQEE VRTIFINQPQ LTKFCNNHVS TAKYNIITFL PRFLYSQFRR AANSFFLFI ALLQQIPDVS PTGRYTTLVP LLFILAVAAI KEIIEDIKRH KADNAVNKKQ TQVLRNGAWE IVHWEKVNVG D IVIIKGKE ...String: GSREFMPTMR RTVSEIRSRA EGYEKTDDVS EKTSLADQEE VRTIFINQPQ LTKFCNNHVS TAKYNIITFL PRFLYSQFRR AANSFFLFI ALLQQIPDVS PTGRYTTLVP LLFILAVAAI KEIIEDIKRH KADNAVNKKQ TQVLRNGAWE IVHWEKVNVG D IVIIKGKE YIPADTVLLS SSEPQAMCYI ETSNLDGETN LKIRQGLPAT SDIKDVDSLM RISGRIECES PNRHLYDFVG NI RLDGHGT VPLGADQILL RGAQLRNTQW VHGIVVYTGH DTKLMQNSTS PPLKLSNVER ITNVQILILF CILIAMSLVC SVG SAIWNR RHSGKDWYLN LNYGGASNFG LNFLTFIILF NNLIPISLLV TLEVVKFTQA YFINWDLDMH YEPTDTAAMA RTSN LNEEL GQVKYIFSDK TGTLTCNVMQ FKKCTIAGVA YGQNSQFGDE KTFSDSSLLE NLQNNHPTAP IICEFLTMMA VCHTA VPER ERDKIIYQAA SPDEGALVRA AKQLNFVFTG RTPDSVIIDS LGQEERYELL NVLEFTSARK RMSVIVRTPS GKLRLY CKG ADTVIYDRLA ETSKYKEITL KHLEQFATEG LRTLCFAVAE ISESDFQEWR AVYQRASTSV QNRLLKLEES YELIEKN LQ LLGATAIEDK LQDQVPETIE TLMKADIKIW ILTGDKQETA INIGHSCKLL KKNMGMIVIN EGSLDGTRET LSRHCTTL G DALRKENDFA LIIDGKTLKY ALTFGVRQYF LDLALSCKAV ICCRVSPLQK SEVVEMVKKQ VKVVTLAIGD GANDVSMIQ TAHVGVGISG NEGLQAANSS DYSIAQFKYL KNLLMIHGAW NYNRVSKCIL YCFYKNIVLY IIEIWFAFVN GFSGQILFER WCIGLYNVM FTAMPPLTLG IFERSCRKEN MLKYPELYKT SQNALDFNTK VFWVHCLNGL FHSVILFWFP LKALQYGTAF G NGKTSDYL LLGNFVYTFV VITVCLKAGL ETSYWTWFSH IAIWGSIALW VVFFGIYSSL WPAIPMAPDM SGEAAMLFSS GV FWMGLLF IPVASLLLDV VYKVIKRTAF KTLVDEVQEL EAKSQDPGAV VLGKSLTERA QLLKNVFKKN HVNLYRSESL QQN LLHGYA FSQDENGIVS QSEVIRAYDT TKQRPDEW |
-Macromolecule #2: Cell cycle control protein 50A
Macromolecule | Name: Cell cycle control protein 50A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 40.727527 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 APCGAIANSM FNDTLELFLI GNDSYPIPIA LKKKGIAWWT DKNVKFRNPP GGDNLEERFK GTTKPVNWLK PV YMLDSDP DNNGFINEDF IVWMRTAALP TFRKLYRLIE RKSDLHPTLP AGRYSLNVTY NYPVHYFDGR KRMILSTISW MGG KNPFLG IAYIAVGSIS FLLGVVLLVI NHKYRNSSNT ADITI |
-Macromolecule #4: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: BEF |
---|---|
Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ![]() ChemComp-BEF: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: Y01 |
---|---|
Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ![]() ChemComp-Y01: |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 2 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 4 mg/mL |
---|---|
Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |