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- EMDB-24212: Cryo-EM structure of ATP13A2 in the E2-Pi state -

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Basic information

Entry
Database: EMDB / ID: EMD-24212
TitleCryo-EM structure of ATP13A2 in the E2-Pi state
Map dataSummed, unsharpened map
Sample
  • Complex: Human ATP13A2 complexed with Pi
    • Protein or peptide: Human ATP13A2 (PARK9)
Function / homology
Function and homology information


polyamine transmembrane transporter activity / ABC-type polyamine transporter activity / polyamine transmembrane transport / spermine transmembrane transport / peptidyl-aspartic acid autophosphorylation / regulation of ubiquitin-specific protease activity / regulation of autophagosome size / extracellular exosome biogenesis / regulation of chaperone-mediated autophagy / P-type ion transporter activity ...polyamine transmembrane transporter activity / ABC-type polyamine transporter activity / polyamine transmembrane transport / spermine transmembrane transport / peptidyl-aspartic acid autophosphorylation / regulation of ubiquitin-specific protease activity / regulation of autophagosome size / extracellular exosome biogenesis / regulation of chaperone-mediated autophagy / P-type ion transporter activity / negative regulation of lysosomal protein catabolic process / regulation of lysosomal protein catabolic process / autophagosome-lysosome fusion / intracellular monoatomic cation homeostasis / regulation of autophagy of mitochondrion / autophagosome organization / protein localization to lysosome / phosphatidic acid binding / multivesicular body membrane / positive regulation of exosomal secretion / ATPase-coupled monoatomic cation transmembrane transporter activity / intracellular zinc ion homeostasis / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / regulation of protein localization to nucleus / cupric ion binding / phosphatidylinositol-3,5-bisphosphate binding / regulation of mitochondrion organization / regulation of endopeptidase activity / lysosomal transport / cellular response to zinc ion / regulation of intracellular protein transport / lipid homeostasis / autophagosome membrane / Ion transport by P-type ATPases / autophagosome / regulation of macroautophagy / cellular response to manganese ion / regulation of neuron apoptotic process / transport vesicle / monoatomic ion transmembrane transport / multivesicular body / lysosomal lumen / positive regulation of protein secretion / transmembrane transport / intracellular calcium ion homeostasis / autophagy / late endosome / cellular response to oxidative stress / late endosome membrane / manganese ion binding / intracellular iron ion homeostasis / vesicle / protein autophosphorylation / 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
: / : / P5-type ATPase cation transporter / P-type ATPase, subfamily V / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily ...: / : / P5-type ATPase cation transporter / P-type ATPase, subfamily V / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Polyamine-transporting ATPase 13A2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSim SI / Park E
CitationJournal: Mol Cell / Year: 2021
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
DepositionJun 9, 2021-
Header (metadata) releaseNov 10, 2021-
Map releaseNov 10, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.115
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.115
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24212.png

Downloads & links

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Map

FileDownload / File: emd_24212.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSummed, unsharpened map
Voxel sizeX=Y=Z: 0.911 Å
Density
Contour LevelBy AUTHOR: 0.115 / Movie #1: 0.115
Minimum - Maximum-0.15894184 - 0.5033347
Average (Standard dev.)0.0013865576 (±0.015937658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 291.52002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9110.9110.911
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z291.520291.520291.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1590.5030.001

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Supplemental data

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Additional map: Summed, sharpened map

Fileemd_24212_additional_1.map
AnnotationSummed, sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_24212_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_24212_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human ATP13A2 complexed with Pi

EntireName: Human ATP13A2 complexed with Pi
Components
  • Complex: Human ATP13A2 complexed with Pi
    • Protein or peptide: Human ATP13A2 (PARK9)

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Supramolecule #1: Human ATP13A2 complexed with Pi

SupramoleculeName: Human ATP13A2 complexed with Pi / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Human ATP13A2 (PARK9)

MacromoleculeName: Human ATP13A2 (PARK9) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.0)
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 605982
FSC plot (resolution estimation)

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