Stark, Holger

[["dc.bibliographiccitation.firstpage","278"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","BIOspektrum"],["dc.bibliographiccitation.lastpage","282"],["dc.bibliographiccitation.volume","24"],["dc.contributor.author","Dybkov, Olexandr"],["dc.contributor.author","Stützer, Alexandra"],["dc.contributor.author","Bertram, Karl"],["dc.contributor.author","Kastner, Berthold"],["dc.contributor.author","Stark, Holger"],["dc.contributor.author","Lührmann, Reinhard"],["dc.contributor.author","Urlaub, Henning"],["dc.date.accessioned","2018-11-15T12:52:38Z"],["dc.date.accessioned","2021-10-27T13:12:42Z"],["dc.date.available","2018-11-15T12:52:38Z"],["dc.date.available","2021-10-27T13:12:42Z"],["dc.date.issued","2018"],["dc.description.abstract","Cryo-electron microscopy (cryo-EM) can solve structures of highly dynamic macromolecular complexes. To characterize less well defined regions in cryo-EM images, cross-linking coupled with mass spectrometry (CX-MS) provides valuable information on the arrangement of domains and amino acids. CX-MS involves covalent linkage of protein residues close to each other and identifying these connections by mass spectrometry. Here, we summarise the advances of CX-MS and its integration with cryo-EM for structural reconstruction."],["dc.identifier.doi","10.1007/s12268-018-0909-6"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/15570"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/91715"],["dc.language.iso","de"],["dc.notes.intern","Migrated from goescholar"],["dc.relation.issn","1868-6249"],["dc.relation.issn","0947-0867"],["dc.relation.orgunit","Fakultät für Chemie"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.title","Protein-Cross-Linking zur Aufklärung von komplexen Strukturen"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","267"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Molecular Cell"],["dc.bibliographiccitation.lastpage","278"],["dc.bibliographiccitation.volume","24"],["dc.contributor.author","Sander, Bjoern"],["dc.contributor.author","Golas, Monika M."],["dc.contributor.author","Makarov, Evgeny M."],["dc.contributor.author","Brahms, Hero"],["dc.contributor.author","Kastner, Berthold"],["dc.contributor.author","Lührmann, Reinhard"],["dc.contributor.author","Stark, Holger"],["dc.date.accessioned","2021-03-05T08:58:09Z"],["dc.date.available","2021-03-05T08:58:09Z"],["dc.date.issued","2006"],["dc.identifier.doi","10.1016/j.molcel.2006.08.021"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80026"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","1097-2765"],["dc.title","Organization of Core Spliceosomal Components U5 snRNA Loop I and U4/U6 Di-snRNP within U4/U6.U5 Tri-snRNP as Revealed by Electron Cryomicroscopy"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","5528"],["dc.bibliographiccitation.issue","14"],["dc.bibliographiccitation.journal","Molecular and Cellular Biology"],["dc.bibliographiccitation.lastpage","5543"],["dc.bibliographiccitation.volume","26"],["dc.contributor.author","Deckert, Jochen"],["dc.contributor.author","Hartmuth, Klaus"],["dc.contributor.author","Boehringer, Daniel"],["dc.contributor.author","Behzadnia, Nastaran"],["dc.contributor.author","Will, Cindy L."],["dc.contributor.author","Kastner, Berthold"],["dc.contributor.author","Stark, Holger"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Lührmann, Reinhard"],["dc.date.accessioned","2021-03-05T08:59:02Z"],["dc.date.available","2021-03-05T08:59:02Z"],["dc.date.issued","2006"],["dc.identifier.doi","10.1128/MCB.00582-06"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80332"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1098-5549"],["dc.relation.issn","0270-7306"],["dc.title","Protein Composition and Electron Microscopy Structure of Affinity-Purified Human Spliceosomal B Complexes Isolated under Physiological Conditions"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","593"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Molecular Cell"],["dc.bibliographiccitation.lastpage","608"],["dc.bibliographiccitation.volume","36"],["dc.contributor.author","Fabrizio, Patrizia"],["dc.contributor.author","Dannenberg, Julia"],["dc.contributor.author","Dube, Prakash"],["dc.contributor.author","Kastner, Berthold"],["dc.contributor.author","Stark, Holger"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Lührmann, Reinhard"],["dc.date.accessioned","2018-11-07T11:21:51Z"],["dc.date.available","2018-11-07T11:21:51Z"],["dc.date.issued","2009"],["dc.description.abstract","Metazoan spliceosomes exhibit an elaborate protein composition required for canonical and alternative splicing. Thus, the minimal set of proteins essential for activation and catalysis remains elusive. We therefore purified in vitro assembled, precatalytic spliceosomal complex B, activated Bact, and step 1 complex C from the simple eukaryote Saccharomyces cerevisiae. Mass spectrometry revealed that yeast spliceosomes contain fewer proteins than metazoans and that each functional stage is very homogeneous. Dramatic compositional changes convert B to Bact, which is composed of similar to 40 evolutionarily conserved proteins that organize the catalytic core. Additional remodeling occurs concomitant with step 1, during which nine proteins are recruited to form complex C. The moderate number of proteins recruited to complex C will allow investigations of the chemical reactions in a fully defined system. Electron microscopy reveals high-quality images of yeast spliceosomes at defined functional stages, indicating that they are well-suited for three-dimensional structure analyses."],["dc.description.sponsorship","European Commission [EURASNET-518238]; Ernst Jung Stiftung"],["dc.identifier.doi","10.1016/j.molcel.2009.09.040"],["dc.identifier.isi","000272534800008"],["dc.identifier.pmid","19941820"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/55879"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Cell Press"],["dc.relation.issn","1097-2765"],["dc.title","The Evolutionarily Conserved Core Design of the Catalytic Activation Step of the Yeast Spliceosome"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","463"],["dc.bibliographiccitation.issue","5"],["dc.bibliographiccitation.journal","Nature Structural & Molecular Biology"],["dc.bibliographiccitation.lastpage","468"],["dc.bibliographiccitation.volume","11"],["dc.contributor.author","Boehringer, Daniel"],["dc.contributor.author","Makarov, Evgeny M."],["dc.contributor.author","Sander, Bjoern"],["dc.contributor.author","Makarova, Olga V."],["dc.contributor.author","Kastner, Berthold"],["dc.contributor.author","Lührmann, Reinhard"],["dc.contributor.author","Stark, Holger"],["dc.date.accessioned","2021-03-05T08:58:30Z"],["dc.date.available","2021-03-05T08:58:30Z"],["dc.date.issued","2004"],["dc.identifier.doi","10.1038/nsmb761"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80158"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1545-9985"],["dc.relation.issn","1545-9993"],["dc.title","Three-dimensional structure of a pre-catalytic human spliceosomal complex B"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","53"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Methods"],["dc.bibliographiccitation.lastpage","55"],["dc.bibliographiccitation.volume","5"],["dc.contributor.author","Kastner, Berthold"],["dc.contributor.author","Fischer, Niels"],["dc.contributor.author","Golas, Monika Mariola"],["dc.contributor.author","Sander, Bjoern"],["dc.contributor.author","Dube, Prakash"],["dc.contributor.author","Boehringer, Daniel"],["dc.contributor.author","Hartmuth, Klaus"],["dc.contributor.author","Deckert, Jochen"],["dc.contributor.author","Hauer, Florian"],["dc.contributor.author","Wolf, Elmar"],["dc.contributor.author","Uchtenhagen, Hannes"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Herzog, Franz"],["dc.contributor.author","Peters, Jan Michael"],["dc.contributor.author","Poerschke, Dietmar"],["dc.contributor.author","Lührmann, Reinhard"],["dc.contributor.author","Stark, Holger"],["dc.date.accessioned","2021-03-05T08:58:29Z"],["dc.date.available","2021-03-05T08:58:29Z"],["dc.date.issued","2007"],["dc.identifier.doi","10.1038/nmeth1139"],["dc.identifier.pii","BFnmeth1139"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80155"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1548-7105"],["dc.relation.issn","1548-7091"],["dc.title","GraFix: sample preparation for single-particle electron cryomicroscopy"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1237"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","Nature Structural & Molecular Biology"],["dc.bibliographiccitation.lastpage","U50"],["dc.bibliographiccitation.volume","16"],["dc.contributor.author","Warkocki, Zbigniew"],["dc.contributor.author","Odenwaelder, Peter"],["dc.contributor.author","Schmitzova, Jana"],["dc.contributor.author","Platzmann, Florian"],["dc.contributor.author","Stark, Holger"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Ficner, Ralf"],["dc.contributor.author","Fabrizio, Patrizia"],["dc.contributor.author","Luehrmann, Reinhard"],["dc.date.accessioned","2017-09-07T11:46:45Z"],["dc.date.available","2017-09-07T11:46:45Z"],["dc.date.issued","2009"],["dc.description.abstract","The spliceosome is a ribonucleoprotein machine that removes introns from pre-mRNA in a two-step reaction. To investigate the catalytic steps of splicing, we established an in vitro splicing complementation system. Spliceosomes stalled before step 1 of this process were purified to near-homogeneity from a temperature-sensitive mutant of the RNA helicase Prp2, compositionally defined, and shown to catalyze efficient step 1 when supplemented with recombinant Prp2, Spp2 and Cwc25, thereby demonstrating that Cwc25 has a previously unknown role in promoting step 1. Step 2 catalysis additionally required Prp16, Slu7, Prp18 and Prp22. Our data further suggest that Prp2 facilitates catalytic activation by remodeling the spliceosome, including destabilizing the SF3a and SF3b proteins, likely exposing the branch site before step 1. Remodeling by Prp2 was confirmed by negative stain EM and image processing. This system allows future mechanistic analyses of spliceosome activation and catalysis."],["dc.identifier.doi","10.1038/nsmb.1729"],["dc.identifier.gro","3143021"],["dc.identifier.isi","000272609200010"],["dc.identifier.pmid","19935684"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/489"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","1545-9993"],["dc.title","Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","296"],["dc.bibliographiccitation.issue","7871"],["dc.bibliographiccitation.journal","Nature"],["dc.bibliographiccitation.lastpage","300"],["dc.bibliographiccitation.volume","596"],["dc.contributor.author","Zhang, Zhenwei"],["dc.contributor.author","Rigo, Norbert"],["dc.contributor.author","Dybkov, Olexandr"],["dc.contributor.author","Fourmann, Jean-Baptiste"],["dc.contributor.author","Will, Cindy L."],["dc.contributor.author","Kumar, Vinay"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Stark, Holger"],["dc.contributor.author","Lührmann, Reinhard"],["dc.date.accessioned","2021-09-01T06:42:22Z"],["dc.date.available","2021-09-01T06:42:22Z"],["dc.date.issued","2021"],["dc.description.abstract","Abstract During the splicing of introns from precursor messenger RNAs (pre-mRNAs), the U2 small nuclear ribonucleoprotein (snRNP) must undergo stable integration into the spliceosomal A complex—a poorly understood, multistep process that is facilitated by the DEAD-box helicase Prp5 (refs. 1–4 ). During this process, the U2 small nuclear RNA (snRNA) forms an RNA duplex with the pre-mRNA branch site (the U2–BS helix), which is proofread by Prp5 at this stage through an unclear mechanism 5 . Here, by deleting the branch-site adenosine (BS-A) or mutating the branch-site sequence of an actin pre-mRNA, we stall the assembly of spliceosomes in extracts from the yeast Saccharomyces cerevisiae directly before the A complex is formed. We then determine the three-dimensional structure of this newly identified assembly intermediate by cryo-electron microscopy. Our structure indicates that the U2–BS helix has formed in this pre-A complex, but is not yet clamped by the HEAT domain of the Hsh155 protein (Hsh155 HEAT ), which exhibits an open conformation. The structure further reveals a large-scale remodelling/repositioning of the U1 and U2 snRNPs during the formation of the A complex that is required to allow subsequent binding of the U4/U6.U5 tri-snRNP, but that this repositioning is blocked in the pre-A complex by the presence of Prp5. Our data suggest that binding of Hsh155 HEAT to the bulged BS-A of the U2–BS helix triggers closure of Hsh155 HEAT , which in turn destabilizes Prp5 binding. Thus, Prp5 proofreads the branch site indirectly, hindering spliceosome assembly if branch-site mutations prevent the remodelling of Hsh155 HEAT . Our data provide structural insights into how a spliceosomal helicase enhances the fidelity of pre-mRNA splicing."],["dc.description.abstract","Abstract During the splicing of introns from precursor messenger RNAs (pre-mRNAs), the U2 small nuclear ribonucleoprotein (snRNP) must undergo stable integration into the spliceosomal A complex—a poorly understood, multistep process that is facilitated by the DEAD-box helicase Prp5 (refs. 1–4 ). During this process, the U2 small nuclear RNA (snRNA) forms an RNA duplex with the pre-mRNA branch site (the U2–BS helix), which is proofread by Prp5 at this stage through an unclear mechanism 5 . Here, by deleting the branch-site adenosine (BS-A) or mutating the branch-site sequence of an actin pre-mRNA, we stall the assembly of spliceosomes in extracts from the yeast Saccharomyces cerevisiae directly before the A complex is formed. We then determine the three-dimensional structure of this newly identified assembly intermediate by cryo-electron microscopy. Our structure indicates that the U2–BS helix has formed in this pre-A complex, but is not yet clamped by the HEAT domain of the Hsh155 protein (Hsh155 HEAT ), which exhibits an open conformation. The structure further reveals a large-scale remodelling/repositioning of the U1 and U2 snRNPs during the formation of the A complex that is required to allow subsequent binding of the U4/U6.U5 tri-snRNP, but that this repositioning is blocked in the pre-A complex by the presence of Prp5. Our data suggest that binding of Hsh155 HEAT to the bulged BS-A of the U2–BS helix triggers closure of Hsh155 HEAT , which in turn destabilizes Prp5 binding. Thus, Prp5 proofreads the branch site indirectly, hindering spliceosome assembly if branch-site mutations prevent the remodelling of Hsh155 HEAT . Our data provide structural insights into how a spliceosomal helicase enhances the fidelity of pre-mRNA splicing."],["dc.identifier.doi","10.1038/s41586-021-03789-5"],["dc.identifier.pii","3789"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/89039"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-455"],["dc.relation.eissn","1476-4687"],["dc.relation.issn","0028-0836"],["dc.title","Structural insights into how Prp5 proofreads the pre-mRNA branch site"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","318"],["dc.bibliographiccitation.issue","7641"],["dc.bibliographiccitation.journal","Nature"],["dc.bibliographiccitation.volume","542"],["dc.contributor.author","Bertram, Karl"],["dc.contributor.author","Agafonov, Dmitry E."],["dc.contributor.author","Liu, Wen-Ti"],["dc.contributor.author","Dybkov, Olexandr"],["dc.contributor.author","Will, Cindy L."],["dc.contributor.author","Hartmuth, Klaus"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Kastner, Berthold"],["dc.contributor.author","Stark, Holger"],["dc.contributor.author","Lührmann, Reinhard"],["dc.date.accessioned","2018-11-07T10:27:23Z"],["dc.date.available","2018-11-07T10:27:23Z"],["dc.date.issued","2017"],["dc.description.abstract","Spliceosome rearrangements facilitated by RNA helicase PRP16 before catalytic step two of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after PRP16 action (C ). The architecture of the catalytic U2-U6 ribonucleoprotein (RNP) core of the human C spliceosome is very similar to that of the yeast pre-Prp16 C complex. However, in C the branched intron region is separated from the catalytic centre by approximately 20 angstrom, and its position close to the U6 small nuclear RNA ACAGA box is stabilized by interactions with the PRP8 RNase H-like and PRP17 WD40 domains. RNA helicase PRP22 is located about 100 angstrom from the catalytic centre, suggesting that it destabilizes the spliced mRNA after step two from a distance. Comparison of the structure of the yeast C and human C complexes reveals numerous RNP rearrangements that are likely to be facilitated by PRP16, including a large-scale movement of the U2 small nuclear RNP."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft [SFB 860]"],["dc.identifier.doi","10.1038/nature21079"],["dc.identifier.isi","000394451600030"],["dc.identifier.pmid","28076346"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/43225"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Nature Publishing Group"],["dc.relation.issn","1476-4687"],["dc.relation.issn","0028-0836"],["dc.title","Cryo-EM structure of a human spliceosome activated for step 2 of splicing"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2528"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","RNA"],["dc.bibliographiccitation.lastpage","2537"],["dc.bibliographiccitation.volume","14"],["dc.contributor.author","Karaduman, Ramazan"],["dc.contributor.author","Dube, Prakash"],["dc.contributor.author","Stark, Holger"],["dc.contributor.author","Fabrizio, Patrizia"],["dc.contributor.author","Kastner, Berthold"],["dc.contributor.author","Lührmann, Reinhard"],["dc.date.accessioned","2018-11-07T11:08:52Z"],["dc.date.available","2018-11-07T11:08:52Z"],["dc.date.issued","2008"],["dc.description.abstract","Protein components of the U6 snRNP (Prp24p and LSm2-8) are thought to act cooperatively in facilitating the annealing of U6 and U4 snRNAs during U4/U6 di-snRNP formation. To learn more about the spatial arrangement of these proteins in S. cerevisiae U6 snRNPs, we investigated the structure of this particle by electron microscopy. U6 snRNPs, purified by affinity chromatography and gradient centrifugation, and then immediately adsorbed to the carbon film support, revealed an open form in which the Prp24 protein and the ring formed by the LSm proteins were visible as two separate morphological domains, while particles stabilized by chemical cross-linking in solution under mild conditions before binding to the carbon film exhibited a compact form, with the two domains in close proximity to one another. In the open form, individual LSm proteins were located by a novel approach employing C-terminal genetic tagging of the LSm proteins with yECitrine. These studies show the Prp24 protein at defined distances from each subunit of the LSm ring, which in turn suggests that the LSm ring is positioned in a consistent manner on the U6 RNA. Furthermore, in agreement with the EM observations, UV cross-linking revealed U6 RNA in contact with the LSm2 protein at the interface between Prp24p and the LSm ring. Further, LSmp-Prp24p interactions may be restricted to the closed form, which appears to represent the solution structure of the U6 snRNP particle."],["dc.identifier.doi","10.1261/rna.1369808"],["dc.identifier.isi","000261398400010"],["dc.identifier.pmid","18971323"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/52888"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Cold Spring Harbor Lab Press, Publications Dept"],["dc.relation.issn","1355-8382"],["dc.title","Structure of yeast U6 snRNPs: Arrangement of Prp24p and the LSm complex as revealed by electron microscopy"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]