1
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Pfister S, Rabl J, Wiegand T, Mattei S, Malär AA, Lecoq L, Seitz S, Bartenschlager R, Böckmann A, Nassal M, Boehringer D, Meier BH. Structural conservation of HBV-like capsid proteins over hundreds of millions of years despite the shift from non-enveloped to enveloped life-style. Nat Commun 2023; 14:1574. [PMID: 36949039 PMCID: PMC10033635 DOI: 10.1038/s41467-023-37068-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/02/2023] [Indexed: 03/24/2023] Open
Abstract
The discovery of nackednaviruses provided new insight into the evolutionary history of the hepatitis B virus (HBV): The common ancestor of HBV and nackednaviruses was non-enveloped and while HBV acquired an envelope during evolution, nackednaviruses remained non-enveloped. We report the capsid structure of the African cichlid nackednavirus (ACNDV), determined by cryo-EM at 3.7 Å resolution. This enables direct comparison with the known capsid structures of HBV and duck HBV, prototypic representatives of the mammalian and avian lineages of the enveloped Hepadnaviridae, respectively. The sequence identity with HBV is 24% and both the ACNDV capsid protein fold and the capsid architecture are very similar to those of the Hepadnaviridae and HBV in particular. Acquisition of the hepadnaviral envelope was thus not accompanied by a major change in capsid structure. Dynamic residues at the spike tip are tentatively assigned by solid-state NMR, while the C-terminal domain is invisible due to dynamics. Solid-state NMR characterization of the capsid structure reveals few conformational differences between the quasi-equivalent subunits of the ACNDV capsid and an overall higher capsid structural disorder compared to HBV. Despite these differences, the capsids of ACNDV and HBV are structurally highly similar despite the 400 million years since their separation.
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Affiliation(s)
- Sara Pfister
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Julius Rabl
- Cryo-EM Knowledge hub, ETH Zurich, 8093, Zurich, Switzerland
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Simone Mattei
- EMBL Imaging Centre, European Molecular Biology Laboratory, EMBL Heidelberg, 69117, Heidelberg, Germany
| | | | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Université de Lyon, 69367, Lyon, France
| | - Stefan Seitz
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Ralf Bartenschlager
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Université de Lyon, 69367, Lyon, France.
| | - Michael Nassal
- Department of Medicine II / Molecular Biology, University of Freiburg, Freiburg im Breisgau, Germany.
| | | | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
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2
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Domanski M, Dedic E, Pérez ME, Cléry A, Campagne S, Uldry AC, Braga S, Heller M, Rabl J, Afanasyev P, Boehringer D, Nováček J, Allain FT, Mühlemann O. 40S hnRNP particles are a novel class of nuclear biomolecular condensates. Nucleic Acids Res 2022; 50:6300-6312. [PMID: 35687109 PMCID: PMC9226511 DOI: 10.1093/nar/gkac457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 11/17/2022] Open
Abstract
Heterogenous nuclear ribonucleoproteins (hnRNPs) are abundant proteins implicated in various steps of RNA processing that assemble on nuclear RNA into larger complexes termed 40S hnRNP particles. Despite their initial discovery 55 years ago, our understanding of these intriguing macromolecular assemblies remains limited. Here, we report the biochemical purification of native 40S hnRNP particles and the determination of their complete protein composition by label-free quantitative mass spectrometry, identifying A-group and C-group hnRNPs as the major protein constituents. Isolated 40S hnRNP particles dissociate upon RNA digestion and can be reconstituted in vitro on defined RNAs in the presence of the individual protein components, demonstrating a scaffolding role for RNA in nucleating particle formation. Finally, we revealed their nanometer scale, condensate-like nature, promoted by intrinsically disordered regions of A-group hnRNPs. Collectively, we identify nuclear 40S hnRNP particles as novel dynamic biomolecular condensates.
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Affiliation(s)
- Michal Domanski
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Emil Dedic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Maria Escura Pérez
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Antoine Cléry
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Sébastien Campagne
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Anne-Christine Uldry
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Murtenstrasse 28, 3008 Bern, Switzerland
| | - Sophie Braga
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Murtenstrasse 28, 3008 Bern, Switzerland
| | - Manfred Heller
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Murtenstrasse 28, 3008 Bern, Switzerland
| | - Julius Rabl
- Cryo-EM Knowledge Hub, ScopeM, Otto Stern Weg 3, ETH Zürich, 8093 Zürich, Switzerland
| | - Pavel Afanasyev
- Cryo-EM Knowledge Hub, ScopeM, Otto Stern Weg 3, ETH Zürich, 8093 Zürich, Switzerland
| | - Daniel Boehringer
- Cryo-EM Knowledge Hub, ScopeM, Otto Stern Weg 3, ETH Zürich, 8093 Zürich, Switzerland
| | - Jiří Nováček
- Cryo-Electron Microscopy and Tomography Core Facility, Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Frédéric T Allain
- Institute of Biochemistry, Department of Biology, ETH Zürich, Hönggerbergring 64, 8093 Zürich, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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3
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Mohamed WI, Schenk AD, Kempf G, Cavadini S, Basters A, Potenza A, Abdul Rahman W, Rabl J, Reichermeier K, Thomä NH. The CRL4 DCAF1 cullin-RING ubiquitin ligase is activated following a switch in oligomerization state. EMBO J 2021; 40:e108008. [PMID: 34595758 PMCID: PMC8591539 DOI: 10.15252/embj.2021108008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 11/09/2022] Open
Abstract
The cullin‐4‐based RING‐type (CRL4) family of E3 ubiquitin ligases functions together with dedicated substrate receptors. Out of the ˜29 CRL4 substrate receptors reported, the DDB1‐ and CUL4‐associated factor 1 (DCAF1) is essential for cellular survival and growth, and its deregulation has been implicated in tumorigenesis. We carried out biochemical and structural studies to examine the structure and mechanism of the CRL4DCAF1 ligase. In the 8.4 Å cryo‐EM map of CRL4DCAF1, four CUL4‐RBX1‐DDB1‐DCAF1 protomers are organized into two dimeric sub‐assemblies. In this arrangement, the WD40 domain of DCAF1 mediates binding with the cullin C‐terminal domain (CTD) and the RBX1 subunit of a neighboring CRL4DCAF1 protomer. This renders RBX1, the catalytic subunit of the ligase, inaccessible to the E2 ubiquitin‐conjugating enzymes. Upon CRL4DCAF1 activation by neddylation, the interaction between the cullin CTD and the neighboring DCAF1 protomer is broken, and the complex assumes an active dimeric conformation. Accordingly, a tetramerization‐deficient CRL4DCAF1 mutant has higher ubiquitin ligase activity compared to the wild‐type. This study identifies a novel mechanism by which unneddylated and substrate‐free CUL4 ligases can be maintained in an inactive state.
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Affiliation(s)
- Weaam I Mohamed
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Andreas D Schenk
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Anja Basters
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Alessandro Potenza
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Julius Rabl
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Kurt Reichermeier
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Genentech, South San Francisco, CA, USA
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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4
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Mohamed WI, Park SL, Rabl J, Leitner A, Boehringer D, Peter M. The human GID complex engages two independent modules for substrate recruitment. EMBO Rep 2021; 22:e52981. [PMID: 34647674 PMCID: PMC8567238 DOI: 10.15252/embr.202152981] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 01/06/2023] Open
Abstract
The human GID (hGID) complex is a conserved E3 ubiquitin ligase regulating diverse biological processes, including glucose metabolism and cell cycle progression. However, the biochemical function and substrate recognition of the multi-subunit complex remain poorly understood. Using biochemical assays, cross-linking mass spectrometry, and cryo-electron microscopy, we show that hGID engages two distinct modules for substrate recruitment, dependent on either WDR26 or GID4. WDR26 and RanBP9 cooperate to ubiquitinate HBP1 in vitro, while GID4 is dispensable for this reaction. In contrast, GID4 functions as an adaptor for the substrate ZMYND19, which surprisingly lacks a Pro/N-end degron. GID4 substrate binding and ligase activity is regulated by ARMC8α, while the shorter ARMC8β isoform assembles into a stable hGID complex that is unable to recruit GID4. Cryo-EM reconstructions of these hGID complexes reveal the localization of WDR26 within a ring-like, tetrameric architecture and suggest that GID4 and WDR26/Gid7 utilize different, non-overlapping binding sites. Together, these data advance our mechanistic understanding of how the hGID complex recruits cognate substrates and provides insights into the regulation of its E3 ligase activity.
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Affiliation(s)
- Weaam I Mohamed
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Sophia L Park
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland.,Life Science Zürich, PhD Program for Molecular Life Sciences, Zürich, Switzerland
| | - Julius Rabl
- Cryo-EM Knowledge Hub (CEMK), Zürich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | | | - Matthias Peter
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
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5
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Rabl J. BRCA1-A and BRISC: Multifunctional Molecular Machines for Ubiquitin Signaling. Biomolecules 2020; 10:biom10111503. [PMID: 33142801 PMCID: PMC7692841 DOI: 10.3390/biom10111503] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
The K63-linkage specific deubiquitinase BRCC36 forms the core of two multi-subunit deubiquitination complexes: BRCA1-A and BRISC. BRCA1-A is recruited to DNA repair foci, edits ubiquitin signals on chromatin, and sequesters BRCA1 away from the site of damage, suppressing homologous recombination by limiting resection. BRISC forms a complex with metabolic enzyme SHMT2 and regulates the immune response, mitosis, and hematopoiesis. Almost two decades of research have revealed how BRCA1-A and BRISC use the same core of subunits to perform very distinct biological tasks.
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Affiliation(s)
- Julius Rabl
- Cryo-EM Knowledge Hub, ETH Zürich, Otto-Stern-Weg 3, HPM C51, 8093 Zürich, Switzerland
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6
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Rabl J, Bunker RD, Schenk AD, Cavadini S, Gill ME, Abdulrahman W, Andrés-Pons A, Luijsterburg MS, Ibrahim AFM, Branigan E, Aguirre JD, Marceau AH, Guérillon C, Bouwmeester T, Hassiepen U, Peters AHFM, Renatus M, Gelman L, Rubin SM, Mailand N, van Attikum H, Hay RT, Thomä NH. Structural Basis of BRCC36 Function in DNA Repair and Immune Regulation. Mol Cell 2019; 75:483-497.e9. [PMID: 31253574 PMCID: PMC6695476 DOI: 10.1016/j.molcel.2019.06.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/30/2019] [Accepted: 05/31/2019] [Indexed: 01/03/2023]
Abstract
In mammals, ∼100 deubiquitinases act on ∼20,000 intracellular ubiquitination sites. Deubiquitinases are commonly regarded as constitutively active, with limited regulatory and targeting capacity. The BRCA1-A and BRISC complexes serve in DNA double-strand break repair and immune signaling and contain the lysine-63 linkage-specific BRCC36 subunit that is functionalized by scaffold subunits ABRAXAS and ABRO1, respectively. The molecular basis underlying BRCA1-A and BRISC function is currently unknown. Here we show that in the BRCA1-A complex structure, ABRAXAS integrates the DNA repair protein RAP80 and provides a high-affinity binding site that sequesters the tumor suppressor BRCA1 away from the break site. In the BRISC structure, ABRO1 binds SHMT2α, a metabolic enzyme enabling cancer growth in hypoxic environments, which we find prevents BRCC36 from binding and cleaving ubiquitin chains. Our work explains modularity in the BRCC36 DUB family, with different adaptor subunits conferring diversified targeting and regulatory functions.
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Affiliation(s)
- Julius Rabl
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Richard D Bunker
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Andreas D Schenk
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Mark E Gill
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Wassim Abdulrahman
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Amparo Andrés-Pons
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Martijn S Luijsterburg
- Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Adel F M Ibrahim
- Centre for Gene Regulation and Expression, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Emma Branigan
- Centre for Gene Regulation and Expression, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Jacob D Aguirre
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Aimee H Marceau
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Claire Guérillon
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen N, Denmark
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Ulrich Hassiepen
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Laurent Gelman
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen N, Denmark
| | - Haico van Attikum
- Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
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7
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Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schübeler D, Iwai S, Sugasawa K, Kurumizaka H, Thomä NH. Publisher Correction: DNA damage detection in nucleosomes involves DNA register shifting. Nature 2019; 571:E6. [PMID: 31239520 DOI: 10.1038/s41586-019-1343-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this Article, in Fig. 1a, the 5' and 3' labels were reversed in the DNA sequence, and Fig. 4 was missing panel labels a-e. These errors have been corrected online.
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Affiliation(s)
- Syota Matsumoto
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Richard D Bunker
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Alessandro Potenza
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Julius Rabl
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Japan
| | - Andreas D Schenk
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center, and Graduate School of Science, Kobe University, Kobe, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
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8
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Weisser M, Voigts-Hoffmann F, Rabl J, Leibundgut M, Ban N. The crystal structure of the eukaryotic 40S ribosomal subunit in complex with eIF1 and eIF1A. Nat Struct Mol Biol 2013; 20:1015-7. [PMID: 23851459 DOI: 10.1038/nsmb.2622] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 05/23/2013] [Indexed: 11/09/2022]
Abstract
Eukaryotic translation initiation factors (eIFs) 1A and 1 are central players in the complex process of start-codon recognition. To improve mechanistic understanding of this process, we determined the crystal structure of the 40S ribosomal subunit in complex with eIF1A and eIF1 from Tetrahymena thermophila at a resolution of 3.7 Å. It reveals the positions of the two factors on the 40S and the conformational changes that accompany their binding.
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Affiliation(s)
- Melanie Weisser
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
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9
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Abstract
Eukaryotic ribosomes are substantially larger and more complex than their bacterial counterparts. Although their core function is conserved, bacterial and eukaryotic protein synthesis differ considerably at the level of initiation. The eukaryotic small ribosomal subunit (40S) plays a central role in this process; it binds initiation factors that facilitate scanning of messenger RNAs and initiation of protein synthesis. We have determined the crystal structure of the Tetrahymena thermophila 40S ribosomal subunit in complex with eukaryotic initiation factor 1 (eIF1) at a resolution of 3.9 angstroms. The structure reveals the fold of the entire 18S ribosomal RNA and of all ribosomal proteins of the 40S subunit, and defines the interactions with eIF1. It provides insights into the eukaryotic-specific aspects of protein synthesis, including the function of eIF1 as well as signaling and regulation mediated by the ribosomal proteins RACK1 and rpS6e.
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Affiliation(s)
- Julius Rabl
- Institute of Molecular Biology and Biophysics, ETH Zürich, Schafmattstrasse 20, 8093 Zürich, Switzerland
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10
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Rabl J, Smith DM, Yu Y, Chang SC, Goldberg AL, Cheng Y. Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases. Mol Cell 2008; 30:360-8. [PMID: 18471981 DOI: 10.1016/j.molcel.2008.03.004] [Citation(s) in RCA: 291] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 02/16/2008] [Accepted: 03/07/2008] [Indexed: 10/22/2022]
Abstract
Substrates enter the cylindrical 20S proteasome through a gated channel that is regulated by the ATPases in the 19S regulatory particle in eukaryotes or the homologous PAN ATPase complex in archaea. These ATPases contain a conserved C-terminal hydrophobic-tyrosine-X (HbYX) motif that triggers gate opening upon ATP binding. Using cryo-electron microscopy, we identified the sites in the archaeal 20S where PAN's C-terminal residues bind and determined the structures of the gate in its closed and open forms. Peptides containing the HbYX motif bind to 20S in the pockets between neighboring alpha subunits where they interact with conserved residues required for gate opening. This interaction induces a rotation in the alpha subunits and displacement of a reverse-turn loop that stabilizes the open-gate conformation. This mechanism differs from that of PA26/28, which lacks the HbYX motif and does not cause alpha subunit rotation. These findings demonstrated how the ATPases' C termini function to facilitate substrate entry.
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Affiliation(s)
- Julius Rabl
- Fachbereich Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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