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- EMDB-24213: Cryo-EM structure of ATP13A2 in the E2-Pi state -

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Basic information

Entry
Database: EMDB / ID: EMD-24213
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 / polyamine transmembrane transport / spermine transmembrane transport / : / ABC-type polyamine transporter activity / regulation of autophagosome size / extracellular exosome biogenesis / regulation of chaperone-mediated autophagy / negative regulation of lysosomal protein catabolic process / regulation of autophagy of mitochondrion ...polyamine transmembrane transporter activity / polyamine transmembrane transport / spermine transmembrane transport / : / ABC-type polyamine transporter activity / regulation of autophagosome size / extracellular exosome biogenesis / regulation of chaperone-mediated autophagy / negative regulation of lysosomal protein catabolic process / regulation of autophagy of mitochondrion / P-type ion transporter activity / regulation of lysosomal protein catabolic process / intracellular monoatomic cation homeostasis / autophagosome-lysosome fusion / protein localization to lysosome / autophagosome organization / phosphatidic acid binding / positive regulation of exosomal secretion / multivesicular body membrane / ATPase-coupled monoatomic cation transmembrane transporter activity / regulation of protein localization to nucleus / intracellular zinc ion homeostasis / cupric ion binding / phosphatidylinositol-3,5-bisphosphate binding / regulation of mitochondrion organization / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / cellular response to zinc ion / lysosomal transport / regulation of intracellular protein transport / lipid homeostasis / Ion transport by P-type ATPases / autophagosome membrane / cellular response to manganese ion / regulation of macroautophagy / transport vesicle / regulation of neuron apoptotic process / multivesicular body / lysosomal lumen / autophagosome / positive regulation of protein secretion / autophagy / intracellular calcium ion homeostasis / late endosome membrane / late endosome / manganese ion binding / cellular response to oxidative stress / monoatomic ion transmembrane transport / vesicle / intracellular iron ion homeostasis / 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: 3.2 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: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24213.png

Downloads & links

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Map

FileDownload / File: emd_24213.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSummed, unsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 320 pix.
= 291.52 Å		0.91 Å/pix.
x 320 pix.
= 291.52 Å		0.91 Å/pix.
x 320 pix.
= 291.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.911 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.29591882 - 0.5969696
Average (Standard dev.)0.00024646556 (±0.014712727)
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-0.2960.5970.000

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Supplemental data

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Additional map: Summed, sharpened map

Fileemd_24213_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_24213_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_24213_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 aff. frugiperda 1 BOLD-2017 (butterflies/moths)
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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 1001323
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.0)
FSC plot (resolution estimation)

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