- EMDB-22263: Structure of P5A-ATPase Spf1, BeF3-bound form -
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Basic information
Entry
Database: EMDB / ID: EMD-22263
Title
Structure of P5A-ATPase Spf1, BeF3-bound form
Map data
unsharpened, lowpass-filtered map
Sample
Complex: P5A-ATPase Spf1 BeF3-bound form
Protein or peptide: P5A-type ATPase
Ligand: BERYLLIUM TRIFLUORIDE ION
Ligand: MAGNESIUM ION
Keywords
P-type ATPase / transmembrane helix dislocase / protein quality control / endoplasmic reticulum / TRANSPORT PROTEIN
Function / homology
Function and homology information
extraction of mislocalized protein from ER membrane / membrane protein dislocase activity / sterol homeostasis / intracellular manganese ion homeostasis / Ion transport by P-type ATPases / P-type ion transporter activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / ATPase-coupled monoatomic cation transmembrane transporter activity / cis-Golgi network / protein hexamerization ...extraction of mislocalized protein from ER membrane / membrane protein dislocase activity / sterol homeostasis / intracellular manganese ion homeostasis / Ion transport by P-type ATPases / P-type ion transporter activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / ATPase-coupled monoatomic cation transmembrane transporter activity / cis-Golgi network / protein hexamerization / phosphatidylinositol-4-phosphate binding / protein unfolding / transmembrane transport / intracellular calcium ion homeostasis / protein transport / endoplasmic reticulum membrane / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding Similarity search - Function
: / P-type ATPase, subfamily V / Cation transport ATPase (P-type) / 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, subfamily V / Cation transport ATPase (P-type) / 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
Journal: Science / Year: 2020 Title: The endoplasmic reticulum P5A-ATPase is a transmembrane helix dislocase. Authors: Michael J McKenna / Sue Im Sim / Alban Ordureau / Lianjie Wei / J Wade Harper / Sichen Shao / Eunyong Park / Abstract: Organelle identity depends on protein composition. How mistargeted proteins are selectively recognized and removed from organelles is incompletely understood. Here, we found that the orphan P5A- ...Organelle identity depends on protein composition. How mistargeted proteins are selectively recognized and removed from organelles is incompletely understood. Here, we found that the orphan P5A-adenosine triphosphatase (ATPase) transporter ATP13A1 (Spf1 in yeast) directly interacted with the transmembrane segment (TM) of mitochondrial tail-anchored proteins. P5A-ATPase activity mediated the extraction of mistargeted proteins from the endoplasmic reticulum (ER). Cryo-electron microscopy structures of Spf1 revealed a large, membrane-accessible substrate-binding pocket that alternately faced the ER lumen and cytosol and an endogenous substrate resembling an α-helical TM. Our results indicate that the P5A-ATPase could dislocate misinserted hydrophobic helices flanked by short basic segments from the ER. TM dislocation by the P5A-ATPase establishes an additional class of P-type ATPase substrates and may correct mistakes in protein targeting or topogenesis.
History
Deposition
Jun 30, 2020
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Header (metadata) release
Sep 23, 2020
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Map release
Sep 23, 2020
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Update
Mar 6, 2024
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Current status
Mar 6, 2024
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Name: P5A-type ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate
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