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Yorodumi- EMDB-9931: Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1 ... -
+Open data
-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) | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information 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 / late endosome membrane / early endosome membrane / cytoplasmic vesicle / positive regulation of cell migration / apical plasma membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / structural molecule activity / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Hiraizumi M / Yamashita K / Nishizawa T / Nureki O | |||||||||
Citation | 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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9931.map.gz | 10.2 MB | EMDB map data format | |
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Header (meta data) | emd-9931-v30.xml emd-9931.xml | 16 KB 16 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9931_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_9931.png | 55.7 KB | ||
Masks | emd_9931_msk_1.map | 67 MB | Mask map | |
Others | emd_9931_half_map_1.map.gz emd_9931_half_map_2.map.gz | 52.1 MB 52.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9931 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9931 | HTTPS FTP |
-Related structure data
Related structure data | 6k7gMC 9932C 9933C 9934C 9935C 9936C 9937C 9938C 9939C 9940C 9941C 9942C 6k7hC 6k7iC 6k7jC 6k7kC 6k7lC 6k7mC 6k7nC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10303 (Title: Cryo-EM structures of human P4-ATPase flippase / Data size: 11.0 TB 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 | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9931.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Mask #1
File | emd_9931_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_9931_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_9931_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ATP8A1-CDC50a
Entire | Name: ATP8A1-CDC50a |
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Components |
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-Supramolecule #1: ATP8A1-CDC50a
Supramolecule | Name: ATP8A1-CDC50a / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: Expi293F / Recombinant plasmid: pcDNA3.4 |
-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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 130.537852 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 40.727527 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #5: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ChemComp-Y01: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |