Sakata, Eri

[["dc.bibliographiccitation.firstpage","1301"],["dc.bibliographiccitation.issue","5"],["dc.bibliographiccitation.journal","Cell Reports"],["dc.bibliographiccitation.lastpage","1315.e5"],["dc.bibliographiccitation.volume","24"],["dc.contributor.author","Eisele, Markus R."],["dc.contributor.author","Reed, Randi G."],["dc.contributor.author","Rudack, Till"],["dc.contributor.author","Schweitzer, Andreas"],["dc.contributor.author","Beck, Florian"],["dc.contributor.author","Nagy, Istvan"],["dc.contributor.author","Pfeifer, Günter"],["dc.contributor.author","Plitzko, Jürgen M."],["dc.contributor.author","Baumeister, Wolfgang"],["dc.contributor.author","Tomko, Robert J."],["dc.contributor.author","Sakata, Eri"],["dc.date.accessioned","2022-03-01T11:45:05Z"],["dc.date.available","2022-03-01T11:45:05Z"],["dc.date.issued","2018"],["dc.identifier.doi","10.1016/j.celrep.2018.07.004"],["dc.identifier.pii","S2211124718310817"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103205"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.issn","2211-1247"],["dc.rights.uri","https://www.elsevier.com/tdm/userlicense/1.0/"],["dc.title","Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","725"],["dc.bibliographiccitation.issue","5"],["dc.bibliographiccitation.journal","Journal of Cell Biology"],["dc.bibliographiccitation.lastpage","740"],["dc.bibliographiccitation.volume","201"],["dc.contributor.author","Fernández Busnadiego, Rubén"],["dc.contributor.author","Asano, Shoh"],["dc.contributor.author","Oprisoreanu, Ana-Maria"],["dc.contributor.author","Sakata, Eri"],["dc.contributor.author","Doengi, Michael"],["dc.contributor.author","Kochovski, Zdravko"],["dc.contributor.author","Zürner, Magdalena"],["dc.contributor.author","Stein, Valentin"],["dc.contributor.author","Schoch, Susanne"],["dc.contributor.author","Baumeister, Wolfgang"],["dc.contributor.author","Lučić, Vladan"],["dc.date.accessioned","2022-03-01T11:46:33Z"],["dc.date.available","2022-03-01T11:46:33Z"],["dc.date.issued","2013"],["dc.description.abstract","Synaptic vesicles are embedded in a complex filamentous network at the presynaptic terminal. Before fusion, vesicles are linked to the active zone (AZ) by short filaments (tethers). The identity of the molecules that form and regulate tethers remains unknown, but Rab3-interacting molecule (RIM) is a prominent candidate, given its central role in AZ organization. In this paper, we analyzed presynaptic architecture of RIM1α knockout (KO) mice by cryo–electron tomography. In stark contrast to previous work on dehydrated, chemically fixed samples, our data show significant alterations in vesicle distribution and AZ tethering that could provide a structural basis for the functional deficits of RIM1α KO synapses. Proteasome inhibition reversed these structural defects, suggesting a functional recovery confirmed by electrophysiological recordings. Altogether, our results not only point to the ubiquitin–proteasome system as an important regulator of presynaptic architecture and function but also show that the tethering machinery plays a critical role in exocytosis, converging into a structural model of synaptic vesicle priming by RIM1α."],["dc.description.abstract","Synaptic vesicles are embedded in a complex filamentous network at the presynaptic terminal. Before fusion, vesicles are linked to the active zone (AZ) by short filaments (tethers). The identity of the molecules that form and regulate tethers remains unknown, but Rab3-interacting molecule (RIM) is a prominent candidate, given its central role in AZ organization. In this paper, we analyzed presynaptic architecture of RIM1α knockout (KO) mice by cryo–electron tomography. In stark contrast to previous work on dehydrated, chemically fixed samples, our data show significant alterations in vesicle distribution and AZ tethering that could provide a structural basis for the functional deficits of RIM1α KO synapses. Proteasome inhibition reversed these structural defects, suggesting a functional recovery confirmed by electrophysiological recordings. Altogether, our results not only point to the ubiquitin–proteasome system as an important regulator of presynaptic architecture and function but also show that the tethering machinery plays a critical role in exocytosis, converging into a structural model of synaptic vesicle priming by RIM1α."],["dc.identifier.doi","10.1083/jcb.201206063"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103710"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.eissn","1540-8140"],["dc.relation.issn","0021-9525"],["dc.title","Cryo–electron tomography reveals a critical role of RIM1α in synaptic vesicle tethering"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","7816"],["dc.bibliographiccitation.issue","28"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences"],["dc.bibliographiccitation.lastpage","7821"],["dc.bibliographiccitation.volume","113"],["dc.contributor.author","Schweitzer, Andreas"],["dc.contributor.author","Aufderheide, Antje"],["dc.contributor.author","Rudack, Till"],["dc.contributor.author","Beck, Florian"],["dc.contributor.author","Pfeifer, Günter"],["dc.contributor.author","Plitzko, Jürgen M."],["dc.contributor.author","Sakata, Eri"],["dc.contributor.author","Schulten, Klaus"],["dc.contributor.author","Förster, Friedrich"],["dc.contributor.author","Baumeister, Wolfgang"],["dc.date.accessioned","2022-03-01T11:46:23Z"],["dc.date.available","2022-03-01T11:46:23Z"],["dc.date.issued","2016"],["dc.description.abstract","Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades polyubiquitylated proteins, and a regulatory particle (RP) containing the AAA-ATPase module. This module controls access to the proteolytic chamber inside the CP and is surrounded by non-ATPase subunits (Rpns) that recognize substrates and deubiquitylate them before unfolding and degradation. The architecture of the 26S holocomplex is highly conserved between yeast and humans. The structure of the human 26S holocomplex described here reveals previously unidentified features of the AAA-ATPase heterohexamer. One subunit, Rpt6, has ADP bound, whereas the other five have ATP in their binding pockets. Rpt6 is structurally distinct from the other five Rpt subunits, most notably in its pore loop region. For Rpns, the map reveals two main, previously undetected, features: the C terminus of Rpn3 protrudes into the mouth of the ATPase ring; and Rpn1 and Rpn2, the largest proteasome subunits, are linked by an extended connection. The structural features of the 26S proteasome observed in this study are likely to be important for coordinating the proteasomal subunits during substrate processing."],["dc.description.abstract","Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades polyubiquitylated proteins, and a regulatory particle (RP) containing the AAA-ATPase module. This module controls access to the proteolytic chamber inside the CP and is surrounded by non-ATPase subunits (Rpns) that recognize substrates and deubiquitylate them before unfolding and degradation. The architecture of the 26S holocomplex is highly conserved between yeast and humans. The structure of the human 26S holocomplex described here reveals previously unidentified features of the AAA-ATPase heterohexamer. One subunit, Rpt6, has ADP bound, whereas the other five have ATP in their binding pockets. Rpt6 is structurally distinct from the other five Rpt subunits, most notably in its pore loop region. For Rpns, the map reveals two main, previously undetected, features: the C terminus of Rpn3 protrudes into the mouth of the ATPase ring; and Rpn1 and Rpn2, the largest proteasome subunits, are linked by an extended connection. The structural features of the 26S proteasome observed in this study are likely to be important for coordinating the proteasomal subunits during substrate processing."],["dc.identifier.doi","10.1073/pnas.1608050113"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103654"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.eissn","1091-6490"],["dc.relation.issn","0027-8424"],["dc.rights.uri","http://www.pnas.org/preview_site/misc/userlicense.xhtml"],["dc.title","Structure of the human 26S proteasome at a resolution of 3.9 Å"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","250"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biochemical and Biophysical Research Communications"],["dc.bibliographiccitation.lastpage","254"],["dc.bibliographiccitation.volume","435"],["dc.contributor.author","Bohn, Stefan"],["dc.contributor.author","Sakata, Eri"],["dc.contributor.author","Beck, Florian"],["dc.contributor.author","Pathare, Ganesh R."],["dc.contributor.author","Schnitger, Jérôme"],["dc.contributor.author","Nágy, Istvan"],["dc.contributor.author","Baumeister, Wolfgang"],["dc.contributor.author","Förster, Friedrich"],["dc.date.accessioned","2022-03-01T11:44:49Z"],["dc.date.available","2022-03-01T11:44:49Z"],["dc.date.issued","2013"],["dc.identifier.doi","10.1016/j.bbrc.2013.04.069"],["dc.identifier.pii","S0006291X13007237"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103129"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.issn","0006-291X"],["dc.title","Localization of the regulatory particle subunit Sem1 in the 26S proteasome"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","140583"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Biochimica et Biophysica Acta. Proteins and Proteomics"],["dc.bibliographiccitation.volume","1869"],["dc.contributor.author","Sakata, Eri"],["dc.contributor.author","Eisele, Markus R."],["dc.contributor.author","Baumeister, Wolfgang"],["dc.date.accessioned","2021-04-14T08:29:04Z"],["dc.date.available","2021-04-14T08:29:04Z"],["dc.date.issued","2021"],["dc.description.abstract","In eukaryotic cells, the ubiquitin-proteasome system serves to remove proteins that are either dysfunctional or no longer needed. The 26S proteasome is a 2.5 MDa multisubunit complex comprising the 20S core particle, where degradation is executed, and one or two regulatory particles which prepare substrates for degradation. Whereas the 20S core particles of several species had been studied extensively by X-ray crystallography, the 26S holocomplex structure had remained elusive for a long time. Recent advances in single-particle cryo-electron microscopy have changed the situation and provided atomic resolution models of this intriguing molecular machine and its dynamics. Besides, cryo-electron tomography enables structural studies in situ, providing molecular resolution images of macromolecules inside pristinely preserved cellular environments. This has greatly contributed to our understanding of proteasome dynamics in the context of cells."],["dc.identifier.doi","10.1016/j.bbapap.2020.140583"],["dc.identifier.pmid","33321258"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/82787"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/130"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.issn","1570-9639"],["dc.relation.workinggroup","RG Sakata (Structural Biology of Protein Quality Control)"],["dc.rights","CC BY-NC-ND 4.0"],["dc.title","Molecular and cellular dynamics of the 26S proteasome"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","overview_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1305"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences"],["dc.bibliographiccitation.lastpage","1310"],["dc.bibliographiccitation.volume","114"],["dc.contributor.author","Wehmer, Marc"],["dc.contributor.author","Rudack, Till"],["dc.contributor.author","Beck, Florian"],["dc.contributor.author","Aufderheide, Antje"],["dc.contributor.author","Pfeifer, Günter"],["dc.contributor.author","Plitzko, Jürgen M."],["dc.contributor.author","Förster, Friedrich"],["dc.contributor.author","Schulten, Klaus"],["dc.contributor.author","Baumeister, Wolfgang"],["dc.contributor.author","Sakata, Eri"],["dc.date.accessioned","2022-03-01T11:46:24Z"],["dc.date.available","2022-03-01T11:46:24Z"],["dc.date.issued","2017"],["dc.description.abstract","In eukaryotic cells, the ubiquitin–proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where proteolysis takes place, and one or two regulatory particles (RPs). The base of the RP is formed by a heterohexameric AAA + ATPase module, which unfolds and translocates substrates into the CP. Applying single-particle cryo-electron microscopy (cryo-EM) and image classification to samples in the presence of different nucleotides and nucleotide analogs, we were able to observe four distinct conformational states (s1 to s4). The resolution of the four conformers allowed for the construction of atomic models of the AAA + ATPase module as it progresses through the functional cycle. In a hitherto unobserved state (s4), the gate controlling access to the CP is open. The structures described in this study allow us to put forward a model for the 26S functional cycle driven by ATP hydrolysis."],["dc.description.abstract","In eukaryotic cells, the ubiquitin–proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where proteolysis takes place, and one or two regulatory particles (RPs). The base of the RP is formed by a heterohexameric AAA + ATPase module, which unfolds and translocates substrates into the CP. Applying single-particle cryo-electron microscopy (cryo-EM) and image classification to samples in the presence of different nucleotides and nucleotide analogs, we were able to observe four distinct conformational states (s1 to s4). The resolution of the four conformers allowed for the construction of atomic models of the AAA + ATPase module as it progresses through the functional cycle. In a hitherto unobserved state (s4), the gate controlling access to the CP is open. The structures described in this study allow us to put forward a model for the 26S functional cycle driven by ATP hydrolysis."],["dc.identifier.doi","10.1073/pnas.1621129114"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103655"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.eissn","1091-6490"],["dc.relation.issn","0027-8424"],["dc.rights.uri","http://www.pnas.org/site/misc/userlicense.xhtml"],["dc.title","Structural insights into the functional cycle of the ATPase module of the 26S proteasome"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","8626"],["dc.bibliographiccitation.issue","28"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences"],["dc.bibliographiccitation.lastpage","8631"],["dc.bibliographiccitation.volume","112"],["dc.contributor.author","Aufderheide, Antje"],["dc.contributor.author","Beck, Florian"],["dc.contributor.author","Stengel, Florian"],["dc.contributor.author","Hartwig, Michaela"],["dc.contributor.author","Schweitzer, Andreas"],["dc.contributor.author","Pfeifer, Günter"],["dc.contributor.author","Goldberg, Alfred L."],["dc.contributor.author","Sakata, Eri"],["dc.contributor.author","Baumeister, Wolfgang"],["dc.contributor.author","Förster, Friedrich"],["dc.date.accessioned","2022-03-01T11:46:23Z"],["dc.date.available","2022-03-01T11:46:23Z"],["dc.date.issued","2015"],["dc.description.abstract","In eukaryotic cells, the 26S proteasome is responsible for the regulated degradation of intracellular proteins. Several cofactors interact transiently with this large macromolecular machine and modulate its function. The deubiquitylating enzyme ubiquitin C-terminal hydrolase 6 [Ubp6; ubiquitin-specific protease (USP) 14 in mammals] is the most abundant proteasome-interacting protein and has multiple roles in regulating proteasome function. Here, we investigate the structural basis of the interaction between Ubp6 and the 26S proteasome in the presence and absence of the inhibitor ubiquitin aldehyde. To this end we have used single-particle electron cryomicroscopy in combination with cross-linking and mass spectrometry. Ubp6 binds to the regulatory particle non-ATPase (Rpn) 1 via its N-terminal ubiquitin-like domain, whereas its catalytic USP domain is positioned variably. Addition of ubiquitin aldehyde stabilizes the binding of the USP domain in a position where it bridges the proteasome subunits Rpn1 and the regulatory particle triple-A ATPase (Rpt) 1. The USP domain binds to Rpt1 in the immediate vicinity of the Ubp6 active site, which may effect its activation. The catalytic triad is positioned in proximity to the mouth of the ATPase module and to the deubiquitylating enzyme Rpn11, strongly implying their functional linkage. On the proteasome side, binding of Ubp6 favors conformational switching of the 26S proteasome into an intermediate-energy conformational state, in particular upon the addition of ubiquitin aldehyde. This modulation of the conformational space of the 26S proteasome by Ubp6 explains the effects of Ubp6 on the kinetics of proteasomal degradation."],["dc.description.abstract","In eukaryotic cells, the 26S proteasome is responsible for the regulated degradation of intracellular proteins. Several cofactors interact transiently with this large macromolecular machine and modulate its function. The deubiquitylating enzyme ubiquitin C-terminal hydrolase 6 [Ubp6; ubiquitin-specific protease (USP) 14 in mammals] is the most abundant proteasome-interacting protein and has multiple roles in regulating proteasome function. Here, we investigate the structural basis of the interaction between Ubp6 and the 26S proteasome in the presence and absence of the inhibitor ubiquitin aldehyde. To this end we have used single-particle electron cryomicroscopy in combination with cross-linking and mass spectrometry. Ubp6 binds to the regulatory particle non-ATPase (Rpn) 1 via its N-terminal ubiquitin-like domain, whereas its catalytic USP domain is positioned variably. Addition of ubiquitin aldehyde stabilizes the binding of the USP domain in a position where it bridges the proteasome subunits Rpn1 and the regulatory particle triple-A ATPase (Rpt) 1. The USP domain binds to Rpt1 in the immediate vicinity of the Ubp6 active site, which may effect its activation. The catalytic triad is positioned in proximity to the mouth of the ATPase module and to the deubiquitylating enzyme Rpn11, strongly implying their functional linkage. On the proteasome side, binding of Ubp6 favors conformational switching of the 26S proteasome into an intermediate-energy conformational state, in particular upon the addition of ubiquitin aldehyde. This modulation of the conformational space of the 26S proteasome by Ubp6 explains the effects of Ubp6 on the kinetics of proteasomal degradation."],["dc.identifier.doi","10.1073/pnas.1510449112"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103653"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.eissn","1091-6490"],["dc.relation.issn","0027-8424"],["dc.rights.uri","http://www.pnas.org/site/misc/userlicense.xhtml"],["dc.title","Structural characterization of the interaction of Ubp6 with the 26S proteasome"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","637"],["dc.bibliographiccitation.issue","5"],["dc.bibliographiccitation.journal","Molecular Cell"],["dc.bibliographiccitation.lastpage","649"],["dc.bibliographiccitation.volume","42"],["dc.contributor.author","Sakata, Eri"],["dc.contributor.author","Stengel, Florian"],["dc.contributor.author","Fukunaga, Keisuke"],["dc.contributor.author","Zhou, Min"],["dc.contributor.author","Saeki, Yasushi"],["dc.contributor.author","Förster, Friedrich"],["dc.contributor.author","Baumeister, Wolfgang"],["dc.contributor.author","Tanaka, Keiji"],["dc.contributor.author","Robinson, Carol V."],["dc.date.accessioned","2022-03-01T11:45:16Z"],["dc.date.available","2022-03-01T11:45:16Z"],["dc.date.issued","2011"],["dc.identifier.doi","10.1016/j.molcel.2011.04.021"],["dc.identifier.pii","S1097276511003388"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103273"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.issn","1097-2765"],["dc.title","The Catalytic Activity of Ubp6 Enhances Maturation of the Proteasomal Regulatory Particle"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]