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- PDB-7n74: Cryo-EM structure of ATP13A2 D508N mutant in the E1-ATP-like state -

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Entry
Database: PDB / ID: 7n74
TitleCryo-EM structure of ATP13A2 D508N mutant in the E1-ATP-like state
ComponentsIsoform 3 of Polyamine-transporting ATPase 13A2
KeywordsTRANSPORT PROTEIN / P-type ATPase / P5B-ATPase / polyamine transporter
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 / P-type ion transporter activity ...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 / P-type ion transporter activity / regulation of autophagy of mitochondrion / regulation of lysosomal protein catabolic process / intracellular monoatomic cation homeostasis / autophagosome-lysosome fusion / autophagosome organization / protein localization to lysosome / positive regulation of exosomal secretion / phosphatidic acid binding / ATPase-coupled monoatomic cation transmembrane transporter activity / multivesicular body membrane / intracellular zinc ion homeostasis / cupric ion binding / regulation of protein localization to nucleus / regulation of mitochondrion organization / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / phosphatidylinositol-3,5-bisphosphate binding / lysosomal transport / regulation of intracellular protein transport / cellular response to zinc ion / lipid homeostasis / Ion transport by P-type ATPases / autophagosome membrane / regulation of macroautophagy / transport vesicle / regulation of neuron apoptotic process / cellular response to manganese ion / 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 / P-type ATPase actuator domain / 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 / P-type ATPase actuator domain / 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
ADENOSINE-5'-TRIPHOSPHATE / CHOLESTEROL HEMISUCCINATE / Polyamine-transporting ATPase 13A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSim, S.I. / Park, E.
Funding support United States, 1items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
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Revision 1.1Dec 1, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
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Assembly

Deposited unit
A: Isoform 3 of Polyamine-transporting ATPase 13A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,9485
Polymers128,4431
Non-polymers1,5054
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 128443.484 Da / Num. of mol.: 1 / Mutation: D508N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP13A2, PARK9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9NQ11, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human ATP13A2 D508N mutant complexed with ATP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / Alignment procedure: COMA FREE
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEM3.7image acquisition
8PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARC2.15classification
13cryoSPARC33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1431882 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058031
ELECTRON MICROSCOPYf_angle_d0.73510986
ELECTRON MICROSCOPYf_dihedral_angle_d7.5981147
ELECTRON MICROSCOPYf_chiral_restr0.11334
ELECTRON MICROSCOPYf_plane_restr0.0061373

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