A. 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 bioenergetic 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 cytosolic 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 how the bioenergetic units that fuel life become to be, the lab members employ structural, functional and evolutionary analysis.

The lab has determined the atomic structures of some of the most complex multi protein assemblies driving key cellular processes, including chlororibosomes, mitoribosomes, photosystems and ATP synthase. The revealed molecular  mechanisms, activities and regulation illuminate how different cells obtain their energy and maintain the bioenergetic balance. From the evolutionary perspective, the achieved understanding of the architecture of these specialized systems provides now a framework to study the mechanisms underlying the development of bioenergetic membranes.

The research is supported by the ERC, Wallenberg Foundation, SSF Future Leaders and EMBO Young Investigator Programmes, Cancer Foundation Junior Investigator Award.


Group members

Rozbeh Baradaran, Researcher

Alexander Mühleip, Postdoc

Yuzuru Itoh, Postdoc

Kock Flygaard, Rasmus, Postdoc

Annemarie Perez Boerema, PhD Student

Vivek Singh, PhD Student

Victor Tobiasson, PhD Student

Fei Wu, PhD Student

Vasileios-Evripidis Kyriakidis, Research Coordinator

Patrick Cottilli, Research Assistant


Research Highlights

Cryo-EM reveals unexpected diversity of photosystems

Structure of a mitochondrial ATP synthase

SciLifeLab, Stockholm University and AstraZeneca use cryo-EM to advance biomedicine


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 feel free to get in touch.



Our research group is at the Science for Life Laboratory (SciLifeLab). SciLifeLab is a joint enterprise of Swedish universities that aims to provide frontline technologies for the academic community and develop cutting-edge research programs. Situated on the expanding Stockholm biomedical campus, SciLifeLab offers the opportunity to work in an internationally competitive and synergistic environment. The center combines technical expertise with advanced knowledge of molecular biology and translational medicine.

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


A selection from Stockholm University publication database
  • 2019. Alexander Mühleip, Sarah E. McComas, Alexey Amunts. eLIFE 8

    The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of Euglena gracilis, a member of the phylum Euglenozoa that also includes human parasites. It features 29 different subunits, 8 of which are newly identified. The membrane region was determined to 2.8 angstrom resolution, enabling the identification of 37 associated lipids, including 25 cardiolipins, which provides insight into protein-lipid interactions and their functional roles. The rotor-stator interface comprises four membrane-embedded horizontal helices, including a distinct subunit a. The dimer interface is formed entirely by phylum-specific components, and a peripherally associated subcomplex contributes to the membrane curvature. The central and peripheral stalks directly interact with each other. Last, the ATPase inhibitory factor 1 (IF1) binds in a mode that is different from human, but conserved in Trypanosomatids.

  • 2019. Anton S. Petrov (et al.). Molecular biology and evolution 36 (2), 207-219

    Mitochondrial ribosomes (mitoribosomes) are essential components of all mitochondria that synthesize proteins encoded by the mitochondrial genome. Unlike other ribosomes, mitoribosomes are highly variable across species. The basis for this diversity is not known. Here, we examine the composition and evolutionary history of mitoribosomes across the phylogenetic tree by combining three-dimensional structural information with a comparative analysis of the secondary structures of mitochondrial rRNAs (mt-rRNAs) and available proteomic data. We generate a map of the acquisition of structural variation and reconstruct the fundamental stages that shaped the evolution of the mitoribosomal large subunit and led to this diversity. Our analysis suggests a critical role for ablation and expansion of rapidly evolving mt-rRNA. These changes cause structural instabilities that are patched by the acquisition of pre-existing compensatory elements, thus providing opportunities for rapid evolution. This mechanism underlies the incorporation of mt-tRNA into the central protuberance of the mammalian mitoribosome, and the altered path of the polypeptide exit tunnel of the yeast mitoribosome. We propose that since the toolkits of elements utilized for structural patching differ between mitochondria of different species, it fosters the growing divergence of mitoribosomes.

  • 2019. Janna M. Bigalke (et al.). Science Advances 5 (7)

    Signaling through the receptor tyrosine kinase RET is essential during normal development. Both gain- and loss-of-function mutations are involved in a variety of diseases, yet the molecular details of receptor activation have remained elusive. We have reconstituted the complete extracellular region of the RET signaling complex together with Neurturin (NRTN) and GFR alpha 2 and determined its structure at 5.7-angstrom resolution by cryo-EM. The proteins form an assembly through RET-GFR alpha 2 and RET-NRTN interfaces. Two key interaction points required for RET extracellular domain binding were observed: (i) the calcium-binding site in RET that contacts GFR alpha 2 domain 3 and (ii) the RET cysteine-rich domain interaction with NRTN. The structure highlights the importance of the RET cysteine-rich domain and allows proposition of a model to explain how complex formation leads to RET receptor dimerization and its activation. This provides a framework for targeting RET activity and for further exploration of mechanisms underlying neurological diseases.

  • 2019. Neha Nirwan (et al.). Nature Communications 10

    The AAA+ GTPase McrB powers DNA cleavage by the endonuclease McrC. The GTPase itself is activated by McrC. The architecture of the GTPase and nuclease complex, and the mechanism of their activation remained unknown. Here, we report a 3.6 angstrom structure of a GTPase-active and DNA-binding deficient construct of McrBC. Two hexameric rings of McrB are bridged by McrC dimer. McrC interacts asymmetrically with McrB protomers and inserts a stalk into the pore of the ring, reminiscent of the gamma subunit complexed to alpha(3)beta(3) of F-1-ATPase. Activation of the GTPase involves conformational changes of residues essential for hydrolysis. Three consecutive nucleotide-binding pockets are occupied by the GTP analogue 5'-guanylyl imidodiphosphate and the next three by GDP, which is suggestive of sequential GTP hydrolysis.

  • 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.

Show all publications by Alexey Amunts at Stockholm University


Last updated: April 11, 2020

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