Structure of yeast RAVE bound to a partial V1 complex

Vacuolar-type ATPases (V-ATPases) are membrane-embedded proton pumps that acidify intracellular compartments in almost all eukaryotic cells. Homologous with ATP synthases, these multi-subunit enzymes consist of a soluble catalytic V1 subcomplex and a membrane-embedded proton-translocating VO subcomplex. The V1 and VO subcomplexes can undergo reversible dissociation to regulate proton pumping, with reassociation of V1 and VO requiring the protein complex known as RAVE (regulator of the ATPase of vacuoles and endosomes). In the yeast Saccharomyces cerevisiae, RAVE consists of subunits Rav1p, Rav2p, and Skp1p. We used electron cryomicroscopy (cryo-EM) to determine a structure of yeast RAVE bound to V1. In the structure, RAVE is a L-shaped complex with Rav2p pointing toward the membrane and Skp1p distant from both the membrane and V1. Only Rav1p interacts with V1, binding to a region of subunit A not found in the corresponding ATP synthase subunit. When bound to RAVE, V1 is in a rotational state suitable for binding the free VO complex, but it is partially disrupted in the structure, missing five of its 16 subunits. Other than these missing subunits and the conformation of the inhibitory subunit H, the V1 complex with RAVE appears poised for reassembly with VO.

• Publication year

  2024

• Venue

  bioRxiv

• Publication date

  2024-07-18

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1101/2024.07.18.604153PMID 39071316PMCID 11648922
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles

  2024influential reference
• CryoEM of V-ATPases: Assembly, disassembly, and inhibition.

  2023cited by this paper
• Structure of ATP synthase under strain during catalysis

  2022cited by this paper
• OpenCell: Endogenous tagging for the cartography of human cellular organization

  2022cited by this paper
• Structural basis of V-ATPase VO region assembly by Vma12p, 21p, and 22p

  2022cited by this paper
• CryoEM Reveals the Complexity and Diversity of ATP Synthases

  2022cited by this paper
• Structure of V-ATPase from citrus fruit

  2022cited by this paper
• Detection and quantification of the vacuolar H+ATPase using the Legionella effector protein SidK

  2021influential reference
• Cryo-EM of the yeast VO complex reveals distinct binding sites for macrolide V-ATPase inhibitors

  2021cited by this paper
• CryoEM of endogenous mammalian V-ATPase interacting with the TLDc protein mEAK-7

  2021cited by this paper
• Coordinated conformational changes in the V1 complex during V-ATPase reversible dissociation

  2021influential reference
• RAVE and Rabconnectin-3 Complexes as Signal Dependent Regulators of Organelle Acidification

  2021influential reference
• Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation

  2021cited by this paper
• Highly accurate protein structure prediction with AlphaFold

  2021cited by this paper
• Defining steps in RAVE-catalyzed V-ATPase assembly using purified RAVE and V-ATPase subcomplexes

  2021influential reference
• The Human Rogdi Protein Is the Functional Homologue of Yeast Rav2 and Can Promote V‐ATPase Assembly

  2021influential reference
• Electron-event representation data enable efficient cryoEM file storage with full preservation of spatial and temporal resolution

  2020cited by this paper
• Structure of V-ATPase from the mammalian brain

  2020cited by this paper
• Interaction between the yeast RAVE complex and Vph1-containing Vo sectors is a central glucose-sensitive interaction required for V-ATPase reassembly

  2020cited by this paper
• Structure and Roles of V-type ATPases.

  2020cited by this paper
• Structural comparison of the vacuolar and Golgi V-ATPases from Saccharomyces cerevisiae

  2019influential reference
• Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction

  2019cited by this paper
• Functional reconstitution of vacuolar H+-ATPase from Vo proton channel and mutant V1-ATPase provides insight into the mechanism of reversible disassembly

  2019cited by this paper
• Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs

  2018cited by this paper
• The 3.5-Å CryoEM Structure of Nanodisc-Reconstituted Yeast Vacuolar ATPase Vo Proton Channel.

  2018cited by this paper
• ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

  2018influential reference
• UCSF ChimeraX: Meeting modern challenges in visualization and analysis

  2018cited by this paper
• Biolayer interferometry of lipid nanodisc‐reconstituted yeast vacuolar H+‐ATPase

  2017cited by this paper
• The crystal structure of human Rogdi provides insight into the causes of Kohlschutter-Tönz Syndrome

  2017influential reference
• WD40 repeat domain proteins: a novel target class?

  2017cited by this paper
• Molecular basis for the binding and modulation of V-ATPase by a bacterial effector protein

  2017cited by this paper
• Crystal structure of yeast V1‐ATPase in the autoinhibited state

  2016cited by this paper
• Atomic model for the membrane-embedded VO motor of a eukaryotic V-ATPase

  2016cited by this paper
• Molecular Interactions and Cellular Itinerary of the Yeast RAVE (Regulator of the H+-ATPase of Vacuolar and Endosomal Membranes) Complex*

  2015influential reference
• Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase

  2015cited by this paper
• The RAVE complex is an isoform-specific V-ATPase assembly factor in yeast

  2014cited by this paper
• Alignment of cryo-EM movies of individual particles by optimization of image translations.

  2014cited by this paper
• Fabrication of carbon films with ∼ 500nm holes for cryo-EM with a direct detector device.

  2014cited by this paper
• Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics*

  2013cited by this paper
• LoQAtE—Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast

  2013cited by this paper
• V-ATPases in osteoclasts: structure, function and potential inhibitors of bone resorption.

  2012cited by this paper
• Structure and function of WD40 domain proteins

  2011influential reference
• Inhibition of Host Vacuolar H+-ATPase Activity by a Legionella pneumophila Effector

  2010cited by this paper
• Regulation of the V-ATPase in kidney epithelial cells: dual role in acid–base homeostasis and vesicle trafficking

  2009cited by this paper
• Function and Subunit Interactions of the N-terminal Domain of Subunit a (Vph1p) of the Yeast V-ATPase*

  2008cited by this paper
• V-ATPase functions in normal and disease processes

  2007cited by this paper
• RAVE Is Essential for the Efficient Assembly of the C Subunit with the Vacuolar H+-ATPase*

  2007cited by this paper
• Vacuolar ATPases: rotary proton pumps in physiology and pathophysiology

  2007cited by this paper
• Skp1p Regulates Soi3p/Rav1p Association with Endosomal Membranes but Is Not Required for Vacuolar ATPase Assembly

  2006influential reference
• Involvement of the Nonhomologous Region of Subunit A of the Yeast V-ATPase in Coupling and in Vivo Dissociation*

  2004cited by this paper
• UCSF Chimera—A visualization system for exploratory research and analysis

  2004cited by this paper
• Coot: model-building tools for molecular graphics.

  2004influential reference
• A novel rabconnectin‐3‐binding protein that directly binds a GDP/GTP exchange protein for Rab3A small G protein implicated in Ca2+‐dependent exocytosis of neurotransmitter

  2003cited by this paper
• Mutational Analysis of the Non-homologous Region of Subunit A of the Yeast V-ATPase*

  2003cited by this paper
• Structural basis for phosphodependent substrate selection and orientation by the SCFCdc4 ubiquitin ligase.

  2003cited by this paper
• Assembly and Regulation of the Yeast Vacuolar H+-ATPase

  2003cited by this paper
• The RAVE Complex Is Essential for Stable Assembly of the Yeast V-ATPase*

  2002influential reference
• Structure of the Cul1–Rbx1–Skp1–F boxSkp2 SCF ubiquitin ligase complex

  2002cited by this paper
• Skp1 forms multiple protein complexes, including RAVE, a regulator of V-ATPase assembly

  2001cited by this paper
• The H Subunit (Vma13p) of the Yeast V-ATPase Inhibits the ATPase Activity of Cytosolic V1 Complexes*

  2000cited by this paper
• Assembly of the Yeast Vacuolar H+-ATPase Occurs in the Endoplasmic Reticulum and Requires a Vma12p/Vma22p Assembly Complex

  1998cited by this paper
• Budding Yeast SKP1 Encodes an Evolutionarily Conserved Kinetochore Protein Required for Cell Cycle Progression

  1996cited by this paper
• Regulation of Plasma Membrane V-ATPase Activity by Dissociation of Peripheral Subunits (*)

  1995cited by this paper
• Disassembly and reassembly of the yeast vacuolar H(+)-ATPase in vivo.

  1995cited by this paper
• Vma21p is a yeast membrane protein retained in the endoplasmic reticulum by a di-lysine motif and is required for the assembly of the vacuolar H(+)-ATPase complex.

  1994cited by this paper
• Isolation of genes encoding the Neurospora vacuolar ATPase. Analysis of vma-1 encoding the 67-kDa subunit reveals homology to other ATPases.

  1988cited by this paper
• The cDNA sequence of the 69-kDa subunit of the carrot vacuolar H+-ATPase. Homology to the beta-chain of F0F1-ATPases.

  1988cited by this paper
• Electronic Reprint Biological Crystallography Phenix : a Comprehensive Python-based System for Macromolecular Structure Solution

  year unknowncited by this paper

• Lysosomes as hubs of metabolic sensing and cellular homeostasis.

  2026cites this paper
• The ROGDI protein mutated in Kohlschutter–Tonz syndrome is a novel subunit of the Rabconnectin-3 complex implicated in V-ATPase assembly

  2025cites this paper
• DMXL1 promotes recruitment of V1-ATPase to lysosomes upon TRPML1 activation

  2025cites this paper
• A heterotrimeric protein complex assembles the metazoan V-ATPase upon dissipation of proton gradients

  2025cites this paper
• V-ATPase and Lysosomal Energy Sensing in Periodontitis and Medicine-Related Osteonecrosis of the Jaw

  2025cites this paper
• The In Situ Structure and Distribution of V-ATPase in C. elegans Apical Membrane Stacks

  2025cites this paper