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


Cryo-EM visualisation of bioenergetic complexes.

Our research group investigates the fundamental question of how proteins are synthesized, folded and assembled into functional multicomponent membrane complexes that drive the cellular energy production.

Living cells ultimately depend on the conversion of energy derived from foodstuff and light into the chemical form of energy. This crucial bioenergetic step is performed in the membrane systems of mitochondria and chloroplasts. Each one of these organelle types has developed dedicated ribosomes that have diverged from the cytoplasmic counterparts. While mitoribosomes synthesize proteins involved in the oxidative phosphorylation, chlororibosomes produce components driving the pohotosynthetic reactions through pigment-protein units. To dissect the mechanism and dynamics of translation, membrane insertion and bioenergetics in organelles, we use cryo-EM.

Our group determined cryo-EM structures of the human mitoribosome with mRNA, tRNAs and translation activators in 8 different functional states, as well as its assembly intermediates. It revealed unique mechanisms of mRNA binding, tRNA translocation and assembly regulation. We also determined structures of the chlororibosome with translation factors that revealed divarication of the exit tunnel and experimental evidence for convergent evolution of ribosomes from chloroplasts and mitochondria.

These studies showed that protein synthesis machineries in organelles have adopted intricate compositions and unique tasks, adding incredible complexity to the records. The achieved understanding of the architecture of these specialized systems provides now a framework to study even more sophisticated questions regarding the assembly and evolution mechanisms of the critical bioenergetic membranes that fuel life.



Structural Biochemitry course, 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

Shintaro Aibara, Postdoc

Yuzuru Itoh, Postdoc

Alexander Mühleip, Postdoc

Annemarie Perez Boerema, PhD Student

Vivek Singh, PhD Student

Victor Tobiasson, PhD Student


Work Opportunities

"Hire very smart people. Leave them alone, but with a tea room to talk. Support them so they have time, & aren't chasing money." Max Perutz                            

If you are interested working in such environment, please contact  Alexey Amunts



Our research group is at the Science for Life Laboratory (SciLifeLab) that serves as a collaboration hub for the top research institutions in the country – Stockholm University, Karolinska Institute, KTH Royal Institute of Technology, Uppsala University. It provides scientists with flexible laboratory space, latest technological tools and funding for ambitious research projects. SciLifeLab hosts the most advanced cryo-EM facilities with dedicated personnel and computational infrastructure for data analysis. Situated on the expanding Stockholm biomedical campus, SciLifeLab offers the oportunity to work in synergistic environment with the University Hospital BioClinicum research centre, and facilitates collaborations with clinicaly oriented pharma industry.

Address: Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna.


Structural Biology colloquia

We gather a discussion group, seminars and annual lecture series to better understand the current practice of cryo-EM, present the most recent developments and applications to interesting biological problems. Please follow SciLifeLab seminar list.


A selection from Stockholm University publication database
  • 2018. Annemarie Perez Boerema (et al.).

    Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast. Chloroplasts evolved ~1.2 billion years ago from an engulfed primordial diazotrophic cyanobacterium, and chlororibosomes are responsible for synthesis of the core proteins driving photochemical reactions. Chlororibosomal activity is spatiotemporally coupled to the synthesis and incorporation of functionally essential co-factors, implying the presence of chloroplast-specific regulatory mechanisms and structural adaptation of the chlororibosome1,2. Despite recent structural information3,4,5,6, some of these aspects remained elusive. To provide new insights into the structural specialities and evolution, we report a comprehensive analysis of the 2.9–3.1 Å resolution electron cryo-microscopy structure of the spinach chlororibosome in complex with its recycling factor and hibernation-promoting factor. The model reveals a prominent channel extending from the exit tunnel to the chlororibosome exterior, structural re-arrangements that lead to increased surface area for translocon binding, and experimental evidence for parallel and convergent evolution of chloro- and mitoribosomes.

  • 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.

Show all publications by Alexey Amunts at Stockholm University

Last updated: June 25, 2018

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