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- EMDB-24220: Cryo-EM structure of ATP13A2 D458N/D962N mutant in the E1-apo sta... -

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Basic information

Entry
Database: EMDB / ID: EMD-24220
TitleCryo-EM structure of ATP13A2 D458N/D962N mutant in the E1-apo state, Conformation 1
Map dataSummed, unsharpened map
Sample
  • Complex: Human ATP13A2 D458N/D962N mutant
    • Protein or peptide: Isoform 3 of Polyamine-transporting ATPase 13A2
  • Ligand: water
KeywordsP-type ATPase / P5B-ATPase / polyamine transporter / TRANSPORT PROTEIN
Function / homologyTranslocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / Isoform 3 of Polyamine-transporting ATPase 13A2
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSim SI / Park E
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
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-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7n75
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24220.png

Downloads & links

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Map

FileDownload / File: emd_24220.map.gz / Format: CCP4 / Size: 103 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.)
1.05 Å/pix.
x 300 pix.
= 314.7 Å		1.05 Å/pix.
x 300 pix.
= 314.7 Å		1.05 Å/pix.
x 300 pix.
= 314.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.049 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18 / Movie #1: 0.18
Minimum - Maximum-0.35924104 - 0.95101506
Average (Standard dev.)0.00081922027 (±0.022388542)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 314.7 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0491.0491.049
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z314.700314.700314.700
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.3590.9510.001

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Supplemental data

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Additional map: Summed, sharpened map

Fileemd_24220_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_24220_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_24220_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 D458N/D962N mutant

EntireName: Human ATP13A2 D458N/D962N mutant
Components
  • Complex: Human ATP13A2 D458N/D962N mutant
    • Protein or peptide: Isoform 3 of Polyamine-transporting ATPase 13A2
  • Ligand: water

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Supramolecule #1: Human ATP13A2 D458N/D962N mutant

SupramoleculeName: Human ATP13A2 D458N/D962N mutant / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 3 of Polyamine-transporting ATPase 13A2

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 128.4425 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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 ALNLVTVVVP 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 INLVITTT VAVLMSRTGP ALVLGRVRPP GALLSVPVLS SLLLQMVLVT GVQLGGYFLT LAQPWFVPLN RTVAAPDNLP NY ENTVVFS LSSFQYLILA AAVSKGAPFR RPLYTNVPFL VALALLSSVL VGLVLVPGLL QGPLALRNIT DTGFKLLLLG LVT LNFVGA FMLESVLDQC LPACLRRLRP KRASKKRFKQ LERELAEQPW PPLPAGPLR

UniProtKB: Isoform 3 of Polyamine-transporting ATPase 13A2

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 - Time: 40 sec. / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 1181866
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.15)
FSC plot (resolution estimation)

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