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  • 1.
    Cheng, Kimberley
    et al.
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Ivanova, Natalia
    Biomedicinskt centrum, Uppsala.
    Scheres, Sjores
    CSIC, Natl Biotechnol Ctr, Biocomp Unit, E-28049 Madrid, Spain .
    Pavlov, Michael Y
    Biomedicinskt centrum, Uppsala.
    Maria Carazo, Jose
    Lund Univ, Mol Biophys KILU.
    Hebert, Hans
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Ehrenberg, Måns
    Biomedicinskt centrum, Uppsala.
    Lindahl, Martin
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    tmRNA-SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes2010In: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 169, no 3, p. 342-348Article in journal (Refereed)
    Abstract [en]

    Bacterial ribosomes stalled on faulty, often truncated, mRNAs lacking stop codons are rescued by trans-translation. It relies on an RNA molecule (tmRNA) capable of replacing the faulty mRNA with its own open reading frame (ORF). Translation of tmRNA ORF results in the tagging of faulty protein for degradation and its release from the ribosome. We used single-particle cryo-electron microscopy to visualize tmRNA together with its helper protein SmpB on the 70S Escherichia coli ribosome in states subsequent to GTP hydrolysis on elongation factor Tu (EF-Tu). Three-dimensional reconstruction and heterogeneity analysis resulted in a 15 A resolution structure of the tmRNA-SmpB complex accommodated in the A site of the ribosome, which shows that SmpB mimics the anticodon- and D-stem of native tRNAs missing in the tRNA-like domain of tmRNA. We conclude that the tmRNA-SmpB complex accommodates in the ribosomal A site very much like an aminoacyl-tRNA during protein elongation. (C) 2009 Elsevier Inc. All rights reserved.

  • 2.
    Elmlund, Hans
    et al.
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Baraznenok, Vera
    Division of Metabolic Diseases, Karolinska Institutet.
    Lindahl, Martin
    Department of Molecular Biophysics, Lund University.
    Samuelsen, Camilla O.
    Department of Genetics, Institute of Molecular Biology, Copenhagen.
    Koeck, Philip J. B.
    KTH, School of Technology and Health (STH).
    Holmberg, Steen
    Department of Genetics, Institute of Molecular Biology, Copenhagen.
    Hebert, Hans
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Gustafsson, Claes M.
    Division of Metabolic Diseases, Karolinska Institutet.
    The cyclin-dependent kinase 8 module sterically blocks Mediator interactions with RNA polymerase II2006In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 103, no 43, p. 15788-15793Article in journal (Refereed)
    Abstract [en]

    CDK8 (cyclin-dependent kinase 8), along with CycC, Med12, and Med13, form a repressive module (the Cdk8 module) that prevents RNA polymerase II (pol II) interactions with Mediator. Here, we report that the ability of the Cdk8 module to prevent pol II interactions is independent of the Cdk8-dependent kinase activity. We use electron microscopy and single-particle reconstruction to demonstrate that the Cdk8 module forms a distinct structural entity that binds to the head and middle region of Mediator, thereby sterically blocking interactions with pol II.

  • 3.
    Elmlund, Hans
    et al.
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Baraznenok, Vera
    Division of Metabolic Diseases, Karolinska Institutet.
    Linder, Tomas
    Division of Metabolic Diseases, Karolinska Institutet.
    Rofougaran, Reza
    Dept. of Medical Biochemistry and Biophysics, Umeå University.
    Hofer, Anders
    Dept. of Medical Biochemistry and Biophysics, Umeå University.
    Hebert, Hans
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Lindahl, Martin
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Gustafsson, Claes M.
    Dept. of Medical Biochemistry and Cell Biology, Göteborg University.
    Visualization of a massive TBP-binding coupled histone-fold domain rearrangement within the general transcription factor IIDArticle in journal (Other academic)
  • 4. Elmlund, Hans
    et al.
    Baraznenok, Vera
    Linder, Tomas
    Szilagyi, Zsolt
    Rofougaran, Reza
    Hofer, Anders
    Hebert, Hans
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Lindahl, Martin Joakim
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Gustafsson, Claes M.
    Cryo-EM Reveals Promoter DNA Binding and Conformational Flexibility of the General Transcription Factor TFIID2009In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 17, no 11, p. 1442-1452Article in journal (Refereed)
    Abstract [en]

    The general transcription factor IID (TFIID) is required for initiation of RNA polymerase II-dependent transcription at many eukaryotic promoters. TFIID comprises the TATA-binding protein (TBP) and several conserved TBP-associated factors (TAFs). Recognition of the core promoter by TFIID assists assembly of the preinitiation complex. Using cryo-electron microscopy in combination with methods for ab initio single-particle reconstruction and heterogeneity analysis, we have produced density maps of two conformational states of Schizosaccharomyces pombe TFIID, containing and lacking TBP. We report that TBP-binding is coupled to a massive histone-fold domain rearrangement. Moreover, docking of the TBP-TAF1(N-terminus) atomic structure to the THID map and reconstruction of a TAF-promoter DNA complex helps to account for TAF-dependent regulation of promoter-TBP and promoter-TAF interactions.

  • 5.
    Elmlund, Hans
    et al.
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Lundqvist, Joakirn
    Lund Univ, Dept Mol Biophys.
    Al-Karadaghi, Salam
    Lund Univ, Dept Mol Biophys.
    Hansson, Mats
    Lund Univ, Dept Biochem.
    Hebert, Hans
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Lindahl, Martin
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    A new cryo-EM single-particle ab initio reconstruction method visualizes secondary structure elements in an ATP-fueled AAA+ motor2008In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 375, no 4, p. 934-947Article in journal (Refereed)
    Abstract [en]

    The generation of ab initio three-dimensional (3D) models is a bottleneck in the studies of large macromolecular assemblies by single-particle cryo-electron microscopy. We describe here a novel method, in which established methods for two-dimensional image processing are combined with newly developed programs for joint rotational 3D alignment of a large number of class averages (RAD) and calculation of 3D volumes from aligned projections (VolRec). We demonstrate the power of the method by reconstructing an similar to 660-kDa ATP-fueled AAA+ motor to 7.5 angstrom resolution, with secondary structure elements identified throughout the structure. We propose the method as a generally applicable automated strategy to obtain 3D reconstructions from unstained single particles imaged in vitreous ice.

  • 6.
    Lindahl, Martin
    KTH, School of Technology and Health (STH), Structural Biotechnology (Closed 20130701).
    tmRNA to the rescue: Structural motives for the salvage of stalled ribosomes2010In: RNA Biology, ISSN 1547-6286, Vol. 7, no 5, p. 577-581Article in journal (Other academic)
    Abstract [en]

    During translation, mRNA molecules are incidentally damaged, leaving the ribosome unable to reach or recognize the stop codon and thus stalled with mRNA and a potentially harmful polypeptide product attached to tRNA in the ribosomal P-site. In bacteria, a process called trans-translation has evolved, where a protein-RNA complex (smpB-tmRNA) mimicks the role of aminoacyl charged tRNA in the ribosomal A-site. The ribosome then resumes protein synthesis guided by an mRNA-like portion of the tmRNA which ends with a stop codon and codes for a peptide sequence susceptible to proteolysis, thus allowing the bacteria to salvage stalled ribosomes and degrade ill-defined and potentially harmful protein products. In this article, we will recollect how structural studies have yielded a model for how the pre-translocation stages of trans-translation employing structural mimicry. We will also discuss possible models for

  • 7.
    Lundqvist, Joakim
    et al.
    Dept. of Molecular Biophysics, Lund University.
    Elmlund, Hans
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Kasperska, Dominika
    Division of Metabolic Diseases, Karolinska Institutet.
    Axelsson, Eva
    Dept. of Biochemistry, Lund University.
    Sirijovski, Nick
    Dept. of Biochemistry, Lund University.
    Hebert, Hans
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Willows, Robert
    Department of Chemistry and Biomolecular Sciences, Macquarie University.
    Hansson, Mats
    Dept. of Biochemistry, Lund University.
    Lindahl, Martin
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Al-Karadaghi, Salam
    Dept. of Molecular Biophysics, Lund University.
    Cryo-electron microscopy reveals an ATP-fueled and Integrin-I mediated conformational transition of the AAA+ activation complex in R. capsulatus Mg-chelataseManuscript (Other academic)
  • 8. Lundqvist, Joakim
    et al.
    Elmlund, Hans
    KTH, School of Technology and Health (STH).
    Wulff, Ragna Peterson
    Berglund, Lisa
    Elmlund, Dominika
    KTH, School of Technology and Health (STH).
    Emanuelsson, Cecilia
    Hebert, Hans
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Willows, Robert D.
    Hansson, Mats
    Lindahl, Martin
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Al-Karadaghi, Salam
    ATP-Induced Conformational Dynamics in the AAA plus Motor Unit of Magnesium Chelatase2010In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 18, no 3, p. 354-365Article in journal (Refereed)
    Abstract [en]

    Mg-chelatase catalyzes the first committed step of the chlorophyll biosynthetic pathway, the ATP-dependent insertion of Mg2+ into protoporphyrin IX (PPIX). Here we report the reconstruction using single-particle cryo-electron microscopy of the complex between subunits BchD and BchI of Rhodobacter capsulatus Mg-chelatase in the presence of ADP, the nonhydrolyzable ATP analog AMPPNP, and ATP at 7.5 angstrom, 14 angstrom, and 13 angstrom resolution, respectively. We show that the two AAA+ modules of the subunits form a unique complex of 3 dimers related by a three-fold axis. The reconstructions demonstrate substantial differences between the conformations of the complex in the presence of ATIP and ADP, and suggest that the C-terminal integrin-I domains of the BchD subunits play a central role in transmitting conformational changes of BchI to BchD. Based on these data a model for the function of magnesium chelatase is proposed.

  • 9. Schagerlöf, Ulrika
    et al.
    Elmlund, Hans
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Gakh, Oleksandr
    Nordlund, Gustav
    Hebert, Hans
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Lindahl, Martin
    KTH, School of Technology and Health (STH), Structural Biotechnology.
    Isaya, Grazia
    Al-Karadaghi, Salam
    Structural basis of the iron storage function of frataxin from single-particle reconstruction of the iron-loaded oligomer2008In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 47, no 17, p. 4948-4954Article in journal (Refereed)
    Abstract [en]

    The mitochondrial protein frataxin plays a central role in mitochondrial iron homeostasis, and frataxin deficiency is responsible for Friedreich ataxia, a neurodegenerative and cardiac disease that affects 1 in 40000 children. Here we present a single-particle reconstruction from cryoelectron microscopic images of iron-loaded 24-subunit oligomeric frataxin particles at 13 and 17 angstrom resolution. Computer-aided classification of particle images showed heterogeneity in particle size, which was hypothesized to result from gradual accumulation of iron within the core structure. Thus, two reconstructions were created from two classes of particles with iron cores of different sizes. The reconstructions show the iron core of frataxin for the first time. Compared to the previous reconstruction of iron-free particles from negatively stained images, the higher resolution of the present reconstruction allowed a more reliable analysis of the overall three-dimensional structure of the 24-meric assembly. This was done after docking the X-ray structure of the frataxin trimer into the EM reconstruction. The structure revealed a close proximity of the suggested ferroxidation sites of different monomers to the site proposed to serve in iron nucleation and mineralization. The model also assigns a new role to the N-terminal helix of frataxin in controlling the channel at the 4-fold axis of the 24-subunit oligomer. The reconstructions show that, together with some common features, frataxin has several unique features which distinguish it from ferritin. These include the overall organization of the oligomers, the way they are stabilized, and the mechanisms of iron core nucleation.

1 - 9 of 9
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