PDB-7n75: Cryo-EM structure of ATP13A2 D458N/D962N mutant in the E1-apo sta...

Basic information

• Entry: Database: PDB / ID: 7n75
• Title: Cryo-EM structure of ATP13A2 D458N/D962N mutant in the E1-apo state, Conformation 1
• Components: Isoform 3 of Polyamine-transporting ATPase 13A2
• Keywords: TRANSPORT PROTEIN / P-type ATPase / P5B-ATPase / polyamine transporter

Function / homology

Function:

regulation of glucosylceramidase 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 / negative regulation of lysosomal protein catabolic process / autophagosome-lysosome fusion / regulation of autophagy of mitochondrion / regulation of lysosomal protein catabolic process / intracellular monoatomic cation homeostasis / autophagosome organization / protein localization to lysosome / phosphatidic acid binding / multivesicular body membrane / positive regulation of exosomal secretion / ATPase-coupled monoatomic cation transmembrane transporter activity / vesicle membrane / intracellular zinc ion homeostasis / regulation of protein localization to nucleus / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / cupric ion binding / regulation of endopeptidase activity / regulation of mitochondrion organization / phosphatidylinositol-3,5-bisphosphate binding / cellular response to zinc ion / lysosomal transport / regulation of intracellular protein transport / lipid homeostasis / autophagosome membrane / Ion transport by P-type ATPases / autophagosome / cellular response to manganese ion / regulation of macroautophagy / transport vesicle / monoatomic ion transmembrane transport / multivesicular body / lysosomal lumen / positive regulation of protein secretion / autophagy / intracellular calcium ion homeostasis / late endosome / manganese ion binding / cellular response to oxidative stress / intracellular iron ion homeostasis / vesicle / protein autophosphorylation / membrane => GO:0016020 / lysosome / neuron projection / lysosomal membrane / neuronal cell body / positive regulation of gene expression / ATP hydrolysis activity / zinc ion binding / ATP binding

Domain/homology:

P5-type ATPase cation transporter / P-type ATPase, subfamily V / 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

Component:

Polyamine-transporting ATPase 13A2

• Biological species: Homo sapiens (human)
• Method: ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
• Authors: Sim, S.I. / Park, E.

Funding support

United States, 1items

Organization	Grant number	Country
Other private		United States

• Citation: Journal: 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 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

Deposition	Jun 9, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 10, 2021	Provider: repository / Type: Initial release
Revision 1.1	Dec 1, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Jun 5, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Assembly

Deposited unit

A: Isoform 3 of Polyamine-transporting ATPase 13A2

Summary:

• 128 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	128,443	1
Polymers	128,443	1
Non-polymers	0	0
Water	54	3

1

Summary:

• Idetical with deposited unit
• defined by author

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555		1

Components

#1: Protein

A Isoform 3 of Polyamine-transporting ATPase 13A2

Details:

Mass: 128442.500 Da / Num. of mol.: 1 / Mutation: D458N, D962N
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: Q9NQ11-3, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate

#2: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: ELECTRON MICROSCOPY
• EM experiment: Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

Sample preparation

• Component: Name: Human ATP13A2 D458N/D962N mutant / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
• Source (natural): Organism: Homo sapiens (human)
• Source (recombinant): Organism: Spodoptera frugiperda (fall armyworm)
• Buffer solution: pH: 7.5
• Specimen: Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
• Specimen support: Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
• Vitrification: Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

Electron microscopy imaging

• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company
• Microscopy: Model: FEI TITAN KRIOS
• Electron gun: Electron source: