Alexey Amunts

Alexey Amunts


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Works at Department of Biochemistry and Biophysics
Telephone 08-16 10 03
Visiting address Science for Life Laboratory, Tomtebodavägen 23, Box 1031, 171 65 Solna
Room SciLifeLab y3
Postal address Institutionen för biokemi och biofysik 106 91 Stockholm


Electron cryo-microscopy visualisation of macromolecules.

The most definitive way to understand molecular mechanisms of a living cell is to directly visualize its components by obtaining their 3D structures. Beyond basic science, structural information on molecules is essential for drug design and optimization of therapeutic compounds. Recent advances in Electron Cryo-Microscopy (cryo-EM) have made it now possible to determine otherwise intractable macro-molecular complexes including membrane proteins at near atomic resolution.

Our group at Science for Life Laboratory in Stockholm further explores the frontiers of the cryo-EM methodology to visualize macromolecules that play key roles in fundamental and medically relevant cellular processes. The lab benefits from the state-of-the-art cryo-EM equipment, including Titan Krios and Talos Arctica armed with the latest generation direct electron detectors, modern computational infrastructure and skilled microscopists.

We are interested in complex questions and technically challenging subjects, for which the molecular mechanisms and dynamics have been least understood. One of the ongoing projects is to characterize the entire mechanism of protein synthesis in mitochondria. We also focus on membrane proteins and bioenergetics related complexes, where intrinsic flexibility and dynamic properties underlie functional characteristics. To realize these proposals, we use a combination of genetic and biochemical methods, while simultaneously developing new methods for direct visualization of molecules in its close to native environment.



Responsible for the course: Structural Biochemitry, 15 ECTS. 

Content: 65 hours of frontal lectures, 18 hours of computational exercise, 16 hours of lab practice (X-tay crystallography and NMR), 14 hours of cryo-EM practice.

Level: given annualy to 25 advanced undergraduate and Master students.

Term: August to October


Group members

Juni Andréll, Researcher

Karin Walldén, Researcher

Shintaro Aibara, Postdoc

Yuzuru Itoh, Postdoc

Narges Mortezaei, Postdoc

Alexander Mühleip, Postdoc

Laura Orellana, Postdoc

Annemarie Perez Boerema, PhD Student

Vivek Singh, PhD Student

Victor Tobiasson, PhD Student

Andre Rosa, Master Student

Shalini Sinha, Research Assistant


Work Opportunities

We offer PhD and Postdoc oportunities as well as short training projects for highly motivated researchers. The lab provides stimulating and collegial environment for people who want to study something important, develop themselves further, work hard and aim high.

– You will be tackling a difficult subject, you are genuinely interested in and enjoying working on.

– You will be offered ample resources, long-term support and collaborations.

– You will be expected to show determination, be proactive, creative and preferably nice to your colleagues.                                      

Please contact  Alexey Amunts


Structural Biology discussion group

We gather a weekly discussion group at SciLifeLab to better understand the current practice of cryo-EM, present the most recent developments and applications to interesting biological problems. The list of upcoming speakers is found here 

We encourage everyone to take active part.


Visiting address

Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden



A selection from Stockholm University publication database
  • 2017. Alan Brown (et al.). Nature Structural & Molecular Biology 24 (10), 866-869

    Mammalian mitochondrial ribosomes (mitoribosomes) have less rRNA content and 36 additional proteins compared with the evolutionarily related bacterial ribosome. These differences make the assembly of mitoribosomes more complex than the assembly of bacterial ribosomes, but the molecular details of mitoribosomal biogenesis remain elusive. Here, we report the structures of two late-stage assembly intermediates of the human mitoribosomal large subunit (mt-LSU) isolated from a native pool within a human cell line and solved by cryo-EM to similar to 3-angstrom resolution. Comparison of the structures reveals insights into the timing of rRNA folding and protein incorporation during the final steps of ribosomal maturation and the evolutionary adaptations that are required to preserve biogenesis after the structural diversification of mitoribosomes. Furthermore, the structures redefine the ribosome silencing factor (RsfS) family as multifunctional biogenesis factors and identify two new assembly factors (L0R8F8 and mt-ACP) not previously implicated in mitoribosomal biogenesis.

  • 2017. Nirupa Desai (et al.). Science 355 (6324), 528-531

    Mitochondria have specialized ribosomes (mitoribosomes) dedicated to the expression of the genetic information encoded by their genomes. Here, using electron cryomicroscopy, we have determined the structure of the 75-component yeast mitoribosome to an overall resolution of 3.3 angstroms. The mitoribosomal small subunit has been built de novo and includes 15S ribosomal RNA (rRNA) and 34 proteins, including 14 without homologs in the evolutionarily related bacterial ribosome. Yeast-specific rRNA and protein elements, including the acquisition of a putatively active enzyme, give the mitoribosome a distinct architecture compared to the mammalian mitoribosome. At an expanded messenger RNA channel exit, there is a binding platform for translational activators that regulate translation in yeast but not mammalian mitochondria. The structure provides insights into the evolution and species-specific specialization of mitochondrial translation.

  • 2017. Donna Matzov (et al.). Nature Communications 8

    Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gram-positive S. aureus lacks an RMF homolog and the structural basis for its 100S formation was not known. Here we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.

  • 2017. Björn O. Forsberg (et al.). IUCrJ 4, 723-727

    The introduction of direct detectors and the automation of data collection in cryo-EM have led to a surge in data, creating new opportunities for advancing computational processing. In particular, on-the-fly workflows that connect data collection with three-dimensional reconstruction would be valuable for more efficient use of cryo-EM and its application as a sample-screening tool. Here, accelerated on-the-fly analysis is reported with optimized organization of the data-processing tools, image acquisition and particle alignment that make it possible to reconstruct the three-dimensional density of the 70S chlororibosome to 3.2 angstrom resolution within 24 h of tissue harvesting. It is also shown that it is possible to achieve even faster processing at comparable quality by imposing some limits to data use, as illustrated by a 3.7 angstrom resolution map that was obtained in only 80 min on a desktop computer. These on-the-fly methods can be employed as an assessment of data quality from small samples and extended to high-throughput approaches.

  • 2016. Martin Ott, Alexey Amunts, Alan Brown. Annual Review of Biochemistry 85, 77-101

    Mitochondria are essential organelles of endosymbiotic origin that are responsible for oxidative phosphorylation within eukaryotic cells. Independent evolution between species has generated mitochondrial genomes that are extremely diverse, with the composition of the vestigial genome determining their translational requirements. Typically, translation within mitochondria is restricted to a few key subunits of the oxidative phosphorylation complexes that are synthesized by dedicated ribosomes (mitoribosomes). The dramatically rearranged mitochondrial genomes, the limited set of transcripts, and the need for the synthesized proteins to coassemble with nuclear-encoded subunits have had substantial consequences for the translation machinery. Recent high-resolution cryo-electron microscopy has revealed the effect of coevolution on the mitoribosome with the mitochondrial genome. In this review, we place the new structural information in the context of the molecular mechanisms of mitochondrial translation and focus on the novel ways protein synthesis is organized and regulated in mitochondria.

Show all publications by Alexey Amunts at Stockholm University


Last updated: December 19, 2017

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