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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24214 | |||||||||
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Title | Cryo-EM structure of ATP13A2 in the BeF-bound E2P-like state | |||||||||
![]() | Summed, unsharpened map | |||||||||
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Function / homology | ![]() 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 / extracellular exosome biogenesis / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Sim SI / Park E | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of polyamine transport by human ATP13A2 (PARK9). Authors: Sue Im Sim / Sören von Bülow / Gerhard Hummer / Eunyong Park / ![]() ![]() Abstract: Polyamines are small, organic polycations that are ubiquitous and essential to all forms of life. Currently, how polyamines are transported across membranes is not understood. Recent studies have ...Polyamines are small, organic polycations that are ubiquitous and essential to all forms of life. Currently, how polyamines are transported across membranes is not understood. Recent studies have suggested that ATP13A2 and its close homologs, collectively known as P5B-ATPases, are polyamine transporters at endo-/lysosomes. Loss-of-function mutations of ATP13A2 in humans cause hereditary early-onset Parkinson's disease. To understand the polyamine transport mechanism of ATP13A2, we determined high-resolution cryoelectron microscopy (cryo-EM) structures of human ATP13A2 in five distinct conformational intermediates, which together, represent a near-complete transport cycle of ATP13A2. The structural basis of the polyamine specificity was revealed by an endogenous polyamine molecule bound to a narrow, elongated cavity within the transmembrane domain. The structures show an atypical transport path for a water-soluble substrate, in which polyamines may exit within the cytosolic leaflet of the membrane. Our study provides important mechanistic insights into polyamine transport and a framework to understand the functions and mechanisms of P5B-ATPases. | |||||||||
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 | ![]() | 62.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.1 KB 22.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.5 KB | Display | ![]() |
Images | ![]() | 57.7 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() ![]() | 118.1 MB 115.8 MB 115.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n70MC ![]() 7n72C ![]() 7n73C ![]() 7n74C ![]() 7n75C ![]() 7n76C ![]() 7n77C ![]() 7n78C C: citing same article ( M: atomic model generated by this map |
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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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Annotation | Summed, unsharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.911 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Summed, sharpened map
File | emd_24214_additional_1.map | ||||||||||||
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Annotation | Summed, sharpened map | ||||||||||||
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Density Histograms |
-Half map: Half map 1
File | emd_24214_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
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Density Histograms |
-Half map: Half map 2
File | emd_24214_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
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Sample components
-Entire : Human ATP13A2 complexed with BeF3
Entire | Name: Human ATP13A2 complexed with BeF3 |
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Components |
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-Supramolecule #1: Human ATP13A2 complexed with BeF3
Supramolecule | Name: Human ATP13A2 complexed with BeF3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Isoform 3 of Polyamine-transporting ATPase 13A2
Macromolecule | Name: Isoform 3 of 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: ![]() ![]() |
Molecular weight | Theoretical: 128.444469 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MSADSSPLVG STPTGYGTLT IGTSIDPLSS SVSSVRLSGY CGSPWRVIGY HVVVWMMAGI PLLLFRWKPL WGVRLRLRPC NLAHAETLV IEIRDKEDSS WQLFTVQVQT EAIGEGSLEP SPQSQAEDGR SQAAVGAVPE GAWKDTAQLH KSEEAKRVLR Y YLFQGQRY ...String: MSADSSPLVG STPTGYGTLT IGTSIDPLSS SVSSVRLSGY CGSPWRVIGY HVVVWMMAGI PLLLFRWKPL WGVRLRLRPC NLAHAETLV IEIRDKEDSS WQLFTVQVQT EAIGEGSLEP SPQSQAEDGR SQAAVGAVPE GAWKDTAQLH KSEEAKRVLR Y YLFQGQRY IWIETQQAFY QVSLLDHGRS CDDVHRSRHG LSLQDQMVRK AIYGPNVISI PVKSYPQLLV DEALNPYYGF QA FSIALWL ADHYYWYALC IFLISSISIC LSLYKTRKQS QTLRDMVKLS MRVCVCRPGG EEEWVDSSEL VPGDCLVLPQ EGG LMPCDA ALVAGECMVN ESSLTGESIP VLKTALPEGL GPYCAETHRR HTLFCGTLIL QARAYVGPHV LAVVTRTGFC TAKG GLVSS ILHPRPINFK FYKHSMKFVA ALSVLALLGT IYSIFILYRN RVPLNEIVIR ALDLVTVVVP PALPAAMTVC TLYAQ SRLR RQGIFCIHPL RINLGGKLQL VCFDKTGTLT EDGLDVMGVV PLKGQAFLPL VPEPRRLPVG PLLRALATCH ALSRLQ DTP VGDPMDLKMV ESTGWVLEEE PAADSAFGTQ VLAVMRPPLW EPQLQAMEEP PVPVSVLHRF PFSSALQRMS VVVAWPG AT QPEAYVKGSP ELVAGLCNPE TVPTDFAQML QSYTAAGYRV VALASKPLPT VPSLEAAQQL TRDTVEGDLS LLGLLVMR N LLKPQTTPVI QALRRTRIRA VMVTGDNLQT AVTVARGCGM VAPQEHLIIV HATHPERGQP ASLEFLPMES PTAVNGVKD PDQAASYTVE PDPRSRHLAL SGPTFGIIVK HFPKLLPKVL VQGTVFARMA PEQKTELVCE LQKLQYCVGM CGDGANDCGA LKAADVGIS LSQAEASVVS PFTSSMASIE CVPMVIREGR CSLDTSFSVF KYMALYSLTQ FISVLILYTI NTNLGDLQFL A IDLVITTT VAVLMSRTGP ALVLGRVRPP GALLSVPVLS SLLLQMVLVT GVQLGGYFLT LAQPWFVPLN RTVAAPDNLP NY ENTVVFS LSSFQYLILA AAVSKGAPFR RPLYTNVPFL VALALLSSVL VGLVLVPGLL QGPLALRNIT DTGFKLLLLG LVT LNFVGA FMLESVLDQC LPACLRRLRP KRASKKRFKQ LERELAEQPW PPLPAGPLR UniProtKB: Polyamine-transporting ATPase 13A2 |
-Macromolecule #2: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ![]() ChemComp-BEF: |
-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: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ![]() ChemComp-Y01: |
-Macromolecule #5: DODECYL-BETA-D-MALTOSIDE
Macromolecule | Name: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 5 / Number of copies: 1 / Formula: LMT |
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Molecular weight | Theoretical: 510.615 Da |
Chemical component information | ![]() ChemComp-LMT: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |