+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32069 | ||||||||||||
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Title | Cryo-EM structure of the human ATP13A2 (SPM-bound E2Pi state) | ||||||||||||
Map data | postprocess_masked.mrc from Relion | ||||||||||||
Sample |
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Function / homology | Function and homology information ABC-type polyamine transporter activity / polyamine transmembrane transport / spermine transmembrane transport / peptidyl-aspartic acid autophosphorylation / regulation of ubiquitin-specific protease activity / polyamine transmembrane transporter activity / regulation of autophagosome size / P-type ion transporter activity / extracellular exosome biogenesis / regulation of chaperone-mediated autophagy ...ABC-type polyamine transporter activity / polyamine transmembrane transport / spermine transmembrane transport / peptidyl-aspartic acid autophosphorylation / regulation of ubiquitin-specific protease activity / polyamine transmembrane transporter activity / regulation of autophagosome size / P-type ion transporter activity / extracellular exosome biogenesis / regulation of chaperone-mediated autophagy / negative regulation of lysosomal protein catabolic process / regulation of autophagy of mitochondrion / regulation of lysosomal protein catabolic process / intracellular monoatomic cation homeostasis / autophagosome-lysosome fusion / autophagosome organization / protein localization to lysosome / phosphatidic acid binding / multivesicular body membrane / positive regulation of exosomal secretion / ATPase-coupled monoatomic cation transmembrane transporter activity / lipid homeostasis / intracellular zinc ion homeostasis / regulation of protein localization to nucleus / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / cupric ion binding / regulation of endopeptidase activity / regulation of mitochondrion organization / phosphatidylinositol-3,5-bisphosphate binding / cellular response to zinc ion / lysosomal transport / regulation of intracellular protein transport / Ion transport by P-type ATPases / autophagosome membrane / autophagosome / cellular response to manganese ion / regulation of macroautophagy / regulation of neuron apoptotic process / transport vesicle / monoatomic ion transmembrane transport / multivesicular body / lysosomal lumen / positive regulation of protein secretion / transmembrane transport / autophagy / intracellular calcium ion homeostasis / late endosome / late endosome membrane / manganese ion binding / cellular response to oxidative stress / intracellular iron ion homeostasis / protein autophosphorylation / vesicle / lysosome / neuron projection / lysosomal membrane / neuronal cell body / positive regulation of gene expression / ATP hydrolysis activity / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.78 Å | ||||||||||||
Authors | Tomita A / Yamashita K / Nishizawa T / Nureki O | ||||||||||||
Funding support | Japan, 3 items
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Citation | Journal: Mol Cell / Year: 2021 Title: Cryo-EM reveals mechanistic insights into lipid-facilitated polyamine export by human ATP13A2. Authors: Atsuhiro Tomita / Takashi Daiho / Tsukasa Kusakizako / Keitaro Yamashita / Satoshi Ogasawara / Takeshi Murata / Tomohiro Nishizawa / Osamu Nureki / Abstract: The cytoplasmic polyamine maintains cellular homeostasis by chelating toxic metal cations, regulating transcriptional activity, and protecting DNA. ATP13A2 was identified as a lysosomal polyamine ...The cytoplasmic polyamine maintains cellular homeostasis by chelating toxic metal cations, regulating transcriptional activity, and protecting DNA. ATP13A2 was identified as a lysosomal polyamine exporter responsible for polyamine release into the cytosol, and its dysfunction is associated with Alzheimer's disease and other neural degradation diseases. ATP13A2 belongs to the P5 subfamily of the P-type ATPase family, but its mechanisms remain unknown. Here, we report the cryoelectron microscopy (cryo-EM) structures of human ATP13A2 under four different conditions, revealing the structural coupling between the polyamine binding and the dephosphorylation. Polyamine is bound at the luminal tunnel and recognized through numerous electrostatic and π-cation interactions, explaining its broad specificity. The unique N-terminal domain is anchored to the lipid membrane to stabilize the E2P conformation, thereby accelerating the E1P-to-E2P transition. These findings reveal the distinct mechanism of P5B ATPases, thereby paving the way for neuroprotective therapy by activating ATP13A2. | ||||||||||||
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_32069.map.gz | 2.1 MB | EMDB map data format | |
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Header (meta data) | emd-32069-v30.xml emd-32069.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32069_fsc.xml | 5.8 KB | Display | FSC data file |
Images | emd_32069.png | 121 KB | ||
Masks | emd_32069_msk_1.map | 14.5 MB | Mask map | |
Others | emd_32069_half_map_1.map.gz emd_32069_half_map_2.map.gz | 11.3 MB 11.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32069 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32069 | HTTPS FTP |
-Related structure data
Related structure data | 7vplMC 7vpiC 7vpjC 7vpkC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10975 (Title: Cryo-EM structure of the human ATP13A2 / Data size: 3.8 TB Data #1: Unaligned movies for E1-ATP state [micrographs - multiframe] Data #2: Unaligned movies for E1P-ADP state [micrographs - multiframe] Data #3: Unaligned movies for SPM-bound E2P state [micrographs - multiframe] Data #4: Unaligned movies for SPM-bound E2Pi state [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_32069.map.gz / Format: CCP4 / Size: 14.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | postprocess_masked.mrc from Relion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34875 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_32069_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: run half2 class001.mrc
File | emd_32069_half_map_1.map | ||||||||||||
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Annotation | run_half2_class001.mrc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: run half1 class001.mrc
File | emd_32069_half_map_2.map | ||||||||||||
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Annotation | run_half1_class001.mrc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ATP13A2
Entire | Name: ATP13A2 |
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Components |
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-Supramolecule #1: ATP13A2
Supramolecule | Name: ATP13A2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Human ATP13A2 in complex with SPM and BeF |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293SGNTI- |
-Macromolecule #1: Polyamine-transporting ATPase 13A2
Macromolecule | Name: Polyamine-transporting ATPase 13A2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 129.313391 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GPSRMSADSS PLVGSTPTGY GTLTIGTSID PLSSSVSSVR LSGYCGSPWR VIGYHVVVWM MAGIPLLLFR WKPLWGVRLR LRPCNLAHA ETLVIEIRDK EDSSWQLFTV QVQTEAIGEG SLEPSPQSQA EDGRSQAAVG AVPEGAWKDT AQLHKSEEAV S VGQKRVLR ...String: GPSRMSADSS PLVGSTPTGY GTLTIGTSID PLSSSVSSVR LSGYCGSPWR VIGYHVVVWM MAGIPLLLFR WKPLWGVRLR LRPCNLAHA ETLVIEIRDK EDSSWQLFTV QVQTEAIGEG SLEPSPQSQA EDGRSQAAVG AVPEGAWKDT AQLHKSEEAV S VGQKRVLR YYLFQGQRYI WIETQQAFYQ VSLLDHGRSC DDVHRSRHGL SLQDQMVRKA IYGPNVISIP VKSYPQLLVD EA LNPYYGF QAFSIALWLA DHYYWYALCI FLISSISICL SLYKTRKQSQ TLRDMVKLSM RVCVCRPGGE EEWVDSSELV PGD CLVLPQ EGGLMPCDAA LVAGECMVNE SSLTGESIPV LKTALPEGLG PYCAETHRRH TLFCGTLILQ ARAYVGPHVL AVVT RTGFC TAKGGLVSSI LHPRPINFKF YKHSMKFVAA LSVLALLGTI YSIFILYRNR VPLNEIVIRA LDLVTVVVPP ALPAA MTVC TLYAQSRLRR QGIFCIHPLR INLGGKLQLV CFDKTGTLTE DGLDVMGVVP LKGQAFLPLV PEPRRLPVGP LLRALA TCH ALSRLQDTPV GDPMDLKMVE STGWVLEEEP AADSAFGTQV LAVMRPPLWE PQLQAMEEPP VPVSVLHRFP FSSALQR MS VVVAWPGATQ PEAYVKGSPE LVAGLCNPET VPTDFAQMLQ SYTAAGYRVV ALASKPLPTV PSLEAAQQLT RDTVEGDL S LLGLLVMRNL LKPQTTPVIQ ALRRTRIRAV MVTGDNLQTA VTVARGCGMV APQEHLIIVH ATHPERGQPA SLEFLPMES PTAVNGVKDP DQAASYTVEP DPRSRHLALS GPTFGIIVKH FPKLLPKVLV QGTVFARMAP EQKTELVCEL QKLQYCVGMC GDGANDCGA LKAADVGISL SQAEASVVSP FTSSMASIEC VPMVIREGRC SLDTSFSVFK YMALYSLTQF ISVLILYTIN T NLGDLQFL AIDLVITTTV AVLMSRTGPA LVLGRVRPPG ALLSVPVLSS LLLQMVLVTG VQLGGYFLTL AQPWFVPLNR TV AAPDNLP NYENTVVFSL SSFQYLILAA AVSKGAPFRR PLYTNVPFLV ALALLSSVLV GLVLVPGLLQ GPLALRNITD TGF KLLLLG LVTLNFVGAF MLESVLDQCL PACLRRLRPK RASKKRFKQL ERELAEQPWP PLPAGPLR |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: TETRAFLUOROALUMINATE ION
Macromolecule | Name: TETRAFLUOROALUMINATE ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ALF |
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Molecular weight | Theoretical: 102.975 Da |
Chemical component information | ChemComp-ALF: |
-Macromolecule #5: SPERMINE
Macromolecule | Name: SPERMINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SPM |
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Molecular weight | Theoretical: 202.34 Da |
Chemical component information | ChemComp-SPM: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-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: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7vpl: |