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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24212 | |||||||||
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Title | Cryo-EM structure of ATP13A2 in the E2-Pi 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 | |||||||||
![]() | ![]() 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 | ![]() | 61.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.8 KB 19.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.5 KB | Display | ![]() |
Images | ![]() | 58.1 KB | ||
Others | ![]() ![]() ![]() | 117.9 MB 115.9 MB 115.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n70C ![]() 7n72C ![]() 7n73C ![]() 7n74C ![]() 7n75C ![]() 7n76C ![]() 7n77C ![]() 7n78C 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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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_24212_additional_1.map | ||||||||||||
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Annotation | Summed, sharpened map | ||||||||||||
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Density Histograms |
-Half map: Half map 1
File | emd_24212_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_24212_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Human ATP13A2 complexed with Pi
Entire | Name: Human ATP13A2 complexed with Pi |
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Components |
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-Supramolecule #1: Human ATP13A2 complexed with Pi
Supramolecule | Name: Human ATP13A2 complexed with Pi / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
-Macromolecule #1: Human ATP13A2 (PARK9)
Macromolecule | Name: Human ATP13A2 (PARK9) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MSADSSPLVG STPTGYGTLT IGTSIDPLSS SVSSVRLSGY CGSPWRVIGY HVVVWMMAGI PLLLFRWKPL WGVRLRLRP CNLAHAETLV IEIRDKEDSS WQLFTVQVQT EAIGEGSLEP SPQSQAEDGR SQAAVGAVPE G AWKDTAQL HKSEEAKRVL RYYLFQGQRY ...String: MSADSSPLVG STPTGYGTLT IGTSIDPLSS SVSSVRLSGY CGSPWRVIGY HVVVWMMAGI PLLLFRWKPL WGVRLRLRP CNLAHAETLV IEIRDKEDSS WQLFTVQVQT EAIGEGSLEP SPQSQAEDGR SQAAVGAVPE G AWKDTAQL HKSEEAKRVL RYYLFQGQRY IWIETQQAFY QVSLLDHGRS CDDVHRSRHG LSLQDQMVRK AI YGPNVIS IPVKSYPQLL VDEALNPYYG FQAFSIALWL ADHYYWYALC IFLISSISIC LSLYKTRKQS QTL RDMVKL SMRVCVCRPG GEEEWVDSSE LVPGDCLVLP QEGGLMPCDA ALVAGECMVN ESSLTGESIP VLKT ALPEG LGPYCAETHR RHTLFCGTLI LQARAYVGPH VLAVVTRTGF CTAKGGLVSS ILHPRPINFK FYKHS MKFV AALSVLALLG TIYSIFILYR NRVPLNEIVI RALDLVTVVV PPALPAAMTV CTLYAQSRLR RQGIFC IHP LRINLGGKLQ LVCFDKTGTL TEDGLDVMGV VPLKGQAFLP LVPEPRRLPV GPLLRALATC HALSRLQ DT PVGDPMDLKM VESTGWVLEE EPAADSAFGT QVLAVMRPPL WEPQLQAMEE PPVPVSVLHR FPFSSALQ R MSVVVAWPGA TQPEAYVKGS PELVAGLCNP ETVPTDFAQM LQSYTAAGYR VVALASKPLP TVPSLEAAQ QLTRDTVEGD LSLLGLLVMR NLLKPQTTPV IQALRRTRIR AVMVTGDNLQ TAVTVARGCG MVAPQEHLII VHATHPERG QPASLEFLPM ESPTAVNGVK DPDQAASYTV EPDPRSRHLA LSGPTFGIIV KHFPKLLPKV L VQGTVFAR MAPEQKTELV CELQKLQYCV GMCGDGANDC GALKAADVGI SLSQAEASVV SPFTSSMASI EC VPMVIRE GRCSLDTSFS VFKYMALYSL TQFISVLILY TINTNLGDLQ FLAIDLVITT TVAVLMSRTG PAL VLGRVR PPGALLSVPV LSSLLLQMVL VTGVQLGGYF LTLAQPWFVP LNRTVAAPDN LPNYENTVVF SLSS FQYLI LAAAVSKGAP FRRPLYTNVP FLVALALLSS VLVGLVLVPG LLQGPLALRN ITDTGFKLLL LGLVT LNFV GAFMLESVLD QCLPACLRRL RPKRASKKRF KQLERELAEQ PWPPLPAGPL R |
-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 - 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 |