EMDB-0647: Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2

Basic information

• Entry: Database: EMDB / ID: EMD-0647
• Title: Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2

Sample

• Complex: Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2
  • Protein or peptide: x 16 types

• Keywords: Proton pump / MEMBRANE PROTEIN

Function / homology

Function:

vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / P-type proton-exporting transporter activity / plasma membrane proton-transporting V-type ATPase complex / pexophagy / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / vacuole organization / protein targeting to vacuole / proton-transporting V-type ATPase complex / fungal-type vacuole / fungal-type vacuole membrane / vacuolar proton-transporting V-type ATPase complex / phosphatidylinositol-4-phosphate binding / vacuolar acidification / proton transmembrane transporter activity / intracellular copper ion homeostasis / endomembrane system / ATP metabolic process / H+-transporting two-sector ATPase / proton transmembrane transport / Neutrophil degranulation / RNA endonuclease activity / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / cell periphery / transmembrane transport / cytoplasmic stress granule / intracellular calcium ion homeostasis / endocytosis / late endosome / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / early endosome / endosome membrane / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / ATP hydrolysis activity / ATP binding / membrane / cytoplasm

Domain/homology:

ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / ATPase, V1 complex, subunit A / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / V-ATPase proteolipid subunit / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit N-term extension / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase

Component:

V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit f / V-type proton ATPase subunit B / V-type proton ATPase subunit E / V-type proton ATPase subunit c'' / V-type proton ATPase subunit c / V-type proton ATPase subunit C / V-type proton ATPase subunit d / V-type proton ATPase subunit D / V-type proton ATPase subunit c' / V-type proton ATPase subunit a, Golgi isoform / V-type proton ATPase subunit F / V-type proton ATPase subunit H / V-type proton ATPase subunit G / V0 assembly protein 1 / V-type proton ATPase subunit e

• Biological species: Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae (strain RM11-1a) (yeast)
• Method: single particle reconstruction / cryo EM / Resolution: 7.0 Å
• Authors: Vasanthakumar T / Bueler SA / Wu D / Beilsten-Edmands V / Robinson CV / Rubinstein JL

Funding support

Canada, 1 items

Organization	Grant number	Country
Canadian Institutes of Health Research (CIHR)	MOP81294	Canada

• Citation: Journal: Proc Natl Acad Sci U S A / Year: 2019; Title: Structural comparison of the vacuolar and Golgi V-ATPases from .; Authors: Thamiya Vasanthakumar / Stephanie A Bueler / Di Wu / Victoria Beilsten-Edmands / Carol V Robinson / John L Rubinstein / ; Abstract: Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal acidification. In mammals, V-ATPase subunit isoforms are differentially targeted to various intracellular compartments or tissues, but how these subunit isoforms influence enzyme activity is not clear. In the yeast , isoform diversity is limited to two different versions of the proton-translocating subunit a: Vph1p, which is targeted to the vacuole, and Stv1p, which is targeted to the Golgi apparatus and endosomes. We show that purified V-ATPase complexes containing Vph1p have higher ATPase activity than complexes containing Stv1p and that the relative difference in activity depends on the presence of lipids. We also show that V complexes containing Stv1p could be readily purified without attached V regions. We used this effect to determine structures of the membrane-embedded V region with Stv1p at 3.1-Å resolution, which we compare with a structure of the V region with Vph1p that we determine to 3.2-Å resolution. These maps reveal differences in the surface charge near the cytoplasmic proton half-channel. Both maps also show the presence of bound lipids, as well as regularly spaced densities that may correspond to ergosterol or bound detergent, around the c-ring.

History

Deposition	Mar 8, 2019	-
Header (metadata) release	Apr 3, 2019	-
Map release	Apr 3, 2019	-
Update	Mar 20, 2024	-
Current status	Mar 20, 2024	Processing site: RCSB / Status: Released