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- EMDB-31627: Cryo EM structure of lysosomal ATPase -

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Basic information

Entry
Database: EMDB / ID: EMD-31627
TitleCryo EM structure of lysosomal ATPase
Map data
Sample
  • Organelle or cellular component: Lysosomal ATPase E2Pi state
    • Protein or peptide: Polyamine-transporting ATPase 13A2
  • Ligand: SPERMINE
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: 3.6 Å
AuthorsZhang SS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21532004, 31570733 China
CitationJournal: Cell Discov / Year: 2021
Title: Cryo-EM structures and transport mechanism of human P5B type ATPase ATP13A2.
Authors: Xudong Chen / Mingze Zhou / Sensen Zhang / Jian Yin / Ping Zhang / Xujun Xuan / Peiyi Wang / Zhiqiang Liu / Boda Zhou / Maojun Yang /
Abstract: Polyamines are important polycations that play critical roles in mammalian cells. ATP13A2 belongs to the orphan P5B adenosine triphosphatases (ATPase) family and has been established as a lysosomal ...Polyamines are important polycations that play critical roles in mammalian cells. ATP13A2 belongs to the orphan P5B adenosine triphosphatases (ATPase) family and has been established as a lysosomal polyamine exporter to maintain the normal function of lysosomes and mitochondria. Previous studies have reported that several human neurodegenerative disorders are related to mutations in the ATP13A2 gene. However, the transport mechanism of ATP13A2 in the lysosome remains unclear. Here, we report the cryo-electron microscopy (cryo-EM) structures of three distinct intermediates of the human ATP13A2, revealing key insights into the spermine (SPM) transport cycle in the lysosome. The transmembrane domain serves as a substrate binding site and the C-terminal domain is essential for protein stability and may play a regulatory role. These findings advance our understanding of the polyamine transport mechanism, the lipid-associated regulation, and the disease-associated mutants of ATP13A2.
History
DepositionAug 4, 2021-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateMar 8, 2023-
Current statusMar 8, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31627.png

Downloads & links

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Map

FileDownload / File: emd_31627.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0979 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.1063843 - 3.7217455
Average (Standard dev.)0.0017141624 (±0.079584904)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 263.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Lysosomal ATPase E2Pi state

EntireName: Lysosomal ATPase E2Pi state
Components
  • Organelle or cellular component: Lysosomal ATPase E2Pi state
    • Protein or peptide: Polyamine-transporting ATPase 13A2
  • Ligand: SPERMINE

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Supramolecule #1: Lysosomal ATPase E2Pi state

SupramoleculeName: Lysosomal ATPase E2Pi state / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Polyamine-transporting ATPase 13A2

MacromoleculeName: 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: 125.889555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSADSSPLVG STPTGYGTLT IGTSIDPLSS SVSSVRLSGY CGSPWRVIGY HVVVWMMAGI PLLLFRWKPL WGVRLRLRPC NLAHAETLV IEIRDKEDSS WQLFTVQVQT EAIGEGSLEP SPQSQAEDGR SQAAVGAVPE GAWKDTAQLH KSEEAVSVGQ K RVLRYYLF ...String:
MSADSSPLVG STPTGYGTLT IGTSIDPLSS SVSSVRLSGY CGSPWRVIGY HVVVWMMAGI PLLLFRWKPL WGVRLRLRPC NLAHAETLV IEIRDKEDSS WQLFTVQVQT EAIGEGSLEP SPQSQAEDGR SQAAVGAVPE GAWKDTAQLH KSEEAVSVGQ K RVLRYYLF QGQRYIWIET QQAFYQVSLL DHGRSCDDVH RSRHGLSLQD QMVRKAIYGP NVISIPVKSY PQLLVDEALN PY YGFQAFS IALWLADHYY WYALCIFLIS SISICLSLYK TRKQSQTLRD MVKLSMRVCV CRPGGEEEWV DSSELVPGDC LVL PQEGGL MPCDAALVAG ECMVNESSLT GESIPVLKTA LPEGLGPYCA ETHRRHTLFC GTLILQARAY VGPHVLAVVT RTGF CTAKG GLVSSILHPR PINFKFYKHS MKFVAALSVL ALLGTIYSIF ILYRNRVPLN EIVIRALDLV TVVVPPALPA AMTVC TLYA QSRLRRQGIF CIHPLRINLG GKLQLVCFDK TGTLTEDGLD VMGVVPLKGQ AFLPLVPEPR RLPVGPLLRA LATCHA LSR LQDTPVGDPM DLKMVESTGP QLQAMEEPPV PVSVLHRFPF SSALQRMSVV VAWPGATQPE AYVKGSPELV AGLCNPE TV PTDFAQMLQS YTAAGYRVVA LASKPLPTVP SLEAAQQLTR DTVEGDLSLL GLLVMRNLLK PQTTPVIQAL RRTRIRAV M VTGDNLQTAV TVARGCGMVA PQEHLIIVHA THPERGQPAS LEFLPMESPT AVNGVKDPDQ AASYTVEPDP RSRHLALSG PTFGIIVKHF PKLLPKVLVQ GTVFARMAPE QKTELVCELQ KLQYCVGMCG DGANDCGALK AADVGISLSQ AEASVVSPFT SSMASIECV PMVIREGRCS LDTSFSVFKY MALYSLTQFI SVLILYTINT NLGDLQFLAI DLVITTTVAV LMSRTGPALV L GRVRPPGA LLSVPVLSSL LLQMVLVTGV QLGGYFLTLA QPWFVPLNRT VAAPDNLPNY ENTVVFSLSS FQYLILAAAV SK GAPFRRP LYTNVPFLVA LALLSSVLVG LVLVPGLLQG PLALRNITDT GFKLLLLGLV TLNFVGAFML ESVLDQCLPA CLR RLRPKR ASKKRFKQLE RELAEQPWPP LPAGPLR

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Macromolecule #2: SPERMINE

MacromoleculeName: SPERMINE / type: ligand / ID: 2 / Number of copies: 1 / Formula: SPM
Molecular weightTheoretical: 202.34 Da
Chemical component information

ChemComp-SPM:
SPERMINE / Spermine

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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: 7.2
VitrificationCryogen name: ETHANE

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 256000

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