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The cyclin-dependent kinase 8 module sterically blocks Mediator interactions with RNA polymerase II
KTH, School of Technology and Health (STH), Structural Biotechnology.
Division of Metabolic Diseases, Karolinska Institutet.
Department of Molecular Biophysics, Lund University.
Department of Genetics, Institute of Molecular Biology, Copenhagen.
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2006 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 103, no 43, 15788-15793 p.Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
2006. Vol. 103, no 43, 15788-15793 p.
Keyword [en]
electron microscopy; transcription; protein structure; yeast; Schizosaccharomyces pombe
National Category
Natural Sciences Natural Sciences
Identifiers
URN: urn:nbn:se:kth:diva-8114DOI: 10.1073/pnas.0607483103ISI: 000241568500013Scopus ID: 2-s2.0-33750481873OAI: oai:DiVA.org:kth-8114DiVA: diva2:13346
Note
QC 20100719Available from: 2008-03-18 Created: 2008-03-18 Last updated: 2010-10-01Bibliographically approved
In thesis
1. Protein structure dynamics and interplay: by single-particle electron microscopy
Open this publication in new window or tab >>Protein structure dynamics and interplay: by single-particle electron microscopy
2008 (English)Doctoral thesis, comprehensive summary (Other scientific)
Abstract [en]

Single-particle cryo-electron microscopy (cryo-EM) is a method capable of obtaining information about the structural organization and dynamics of large macromolecular assemblies. In the late nineties, the method was suggested to have the potential of generating “atomic resolution” reconstructions of particles above a certain mass. However, visualization of secondary structure elements in cryo-EM reconstructions has so far been achieved mainly for highly symmetrical macromolecular assemblies or by using previously existing X-ray structures to solve the initial alignment problem. A factor that severely limits the resolution for low-symmetry (point group symmetry Cn) particles is the problem of ab initio three-dimensional alignment of cryo-EM projection images of proteins in vitreous ice.

A more general problem in the field of molecular biology is the study of heterogeneous structural properties of particles in preparations of purified macromolecular complexes. If not resolved, structural heterogeneity limits the achievable resolution of a cryo-EM reconstruction and makes correct biological interpretation difficult. If resolved, the heterogeneity instead offers a tremendous biological insight into the dynamic behaviour of a structure, and statistical information about partitioning over subpopulations with distinct structural features within the ensemble of particles may be gained.

This thesis adds to the existing body of methods in the field of single-particle cryo-EM by addressing the problem of ab initio rotational alignment and the problem of resolving structural heterogeneity without using a priori information about the structural variability within large populations of cryo-EM projections of unstained proteins. The thesis aims at making the single-particle cryo-EM method a generally applicable tool for generating subnanometer resolution reconstructions and perform heterogeneity analysis of biological macromolecules.

Place, publisher, year, edition, pages
Stockholm: KTH, 2008. 83 p.
Series
Trita-STH : report, ISSN 1653-3836 ; 2008:1
Keyword
biophysics, biochemistry, molecular
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-4669 (URN)978-91-7178-892-4 (ISBN)
Public defence
2008-04-04, Hörsallen plan 4, Novum, Flemingsberg, Huddinge, 13:00
Opponent
Supervisors
Note
QC 20100719Available from: 2008-03-18 Created: 2008-03-18 Last updated: 2010-10-01Bibliographically approved

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