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Structure paper

TitleStructural mechanisms for gating and ion selectivity of the human polyamine transporter ATP13A2.
Journal, issue, pagesMol Cell, Vol. 81, Issue 22, Page 4650-44662.e4, Year 2021
Publish dateNov 18, 2021
AuthorsJordan Tillinghast / Sydney Drury / Darren Bowser / Alana Benn / Kenneth Pak Kin Lee /
PubMed AbstractMutations in ATP13A2, also known as PARK9, cause a rare monogenic form of juvenile-onset Parkinson's disease named Kufor-Rakeb syndrome and other neurodegenerative diseases. ATP13A2 encodes a ...Mutations in ATP13A2, also known as PARK9, cause a rare monogenic form of juvenile-onset Parkinson's disease named Kufor-Rakeb syndrome and other neurodegenerative diseases. ATP13A2 encodes a neuroprotective P5B P-type ATPase highly enriched in the brain that mediates selective import of spermine ions from lysosomes into the cytosol via an unknown mechanism. Here we present three structures of human ATP13A2 bound to an ATP analog or to spermine in the presence of phosphomimetics determined by cryoelectron microscopy. ATP13A2 autophosphorylation opens a lysosome luminal gate to reveal a narrow lumen access channel that holds a spermine ion in its entrance. ATP13A2's architecture suggests physical principles underlying selective polyamine transport and anticipates a "pump-channel" intermediate that could function as a counter-cation conduit to facilitate lysosome acidification. Our findings establish a firm foundation to understand ATP13A2 mutations associated with disease and bring us closer to realizing ATP13A2's potential in neuroprotective therapy.
External linksMol Cell / PubMed:34715014
MethodsEM (single particle)
Resolution2.7 - 3.0 Å
Structure data

23683

7m5v

EMDB-23683, PDB-7m5v:
human ATP13A2 in the AMPPNP-bound occluded state
Method: EM (single particle) / Resolution: 2.9 Å

23684

7m5x

EMDB-23684, PDB-7m5x:
Human ATP13A2 in the outward-facing E2 state bound to spermine and beryllium fluoride
Method: EM (single particle) / Resolution: 2.7 Å

23685

7m5y

EMDB-23685, PDB-7m5y:
human ATP13A2 in the outward-facing E2 state bound to spermine and magnesium fluoride
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-1DO:
1-DODECANOL

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

ChemComp-D10:
DECANE

ChemComp-D12:
DODECANE

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-EUJ:
(2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate

ChemComp-HOH:
WATER

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-CLR:
CHOLESTEROL

ChemComp-C14:
TETRADECANE

ChemComp-SPK:
SPERMINE (FULLY PROTONATED FORM)

ChemComp-MF4:
TETRAFLUOROMAGNESATE(2-)

Source
  • homo sapiens (human)
KeywordsTRANSPORT PROTEIN / ion transport occluded state / MEMBRANE PROTEIN / ion transport inhibited state

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