Principal Investigator Benjamin Engel

Structural Cell Biology 

Molecular Architecture of the Cell

Cells accomplish the biochemical reactions of life by concentrating their proteins into a variety of subcellular compartments called organelles.  Our group explores the relationship between the form of the organelle and the function of its resident macromolecules.  How does organelle architecture direct molecular function, and reciprocally, how do macromolecules sculpt and shape organelles?

To investigate these questions, our group uses cryo-electron tomography (cryo-ET) to directly visualize macromolecules “in situ”, within the native cellular environment.  First, we rapidly freeze the cells in non-crystalline vitreous ice, preserving them in a state of suspended animation.  Next, we use a focused ion beam to thin the cells, followed by cryo-ET to acquire 3D images (called tomograms) of the native cellular interior with molecular resolution.  These tomograms enable us to solve molecular structures directly within the cell, at sufficient resolution to distinguish different conformational states and interaction partners.  We then map these structures back into the cellular volume with nanometer precision, allowing us to analyze molecular organization within the cell at the scale of single molecules.

While we are broadly interested in all questions of cellular architecture, we concentrate on two topics:

1) How does cellular architecture impact human health? Here, we investigate how diseases alter cellular compartments including the mitochondrion (the cell’s power plant), the cilium (the cell’s signaling antenna), and the Golgi (the cell’s post office).

2) How does cellular architecture respond to the Earth’s changing environment? Here, we examine how the chloroplast (the cell’s solar panel) adapts to environmental stresses caused by climate change. We study a wide range of photosynthetic organisms and are particularly interested in marine algae, which fix about half of the Earth’s CO2.

For a full description of our research, please see our group website:



Structural Cell Biology at HMGU

We aim to leverage the full power of cryo-electron microscopy towards the goals of improving human health and understanding how photosynthetic organisms respond to climate change. This revolutionary technology enables:

  • Atomic-resolution structure determination of purified molecular complexes.
  • “In situ” tomography to visualize molecular structures within the native cellular environment.
  • Correlation with light microscopy, bridging the scales between atoms and cells.

Dr. Benjamin Engel

Principal Investigator, Structural Cell Biology

Ben was trained as a Cell Biologist at UC San Francisco, and later was immersed in Structural Biology as a postdoc and project leader at the Max Planck Institute of Biochemistry.  Combining these backgrounds, Ben and his team use in situ cryo-electron tomography to capture a structural view of cell biology.  This technique directly images the structures of molecular complexes within the native cellular environment, revealing the architecture of the cell with exquisite detail. 


Dr. Benjamin Engel

Google Scholar


Principal Investigator, Helmholtz Pioneer Campus

Postdoc (Project Leader starting 2015), Wolfgang Baumeister, MPI of Biochemistry We are using focused ion beam milling and cryo-electron tomography to study the in situ structural biology of macromolecules within native-state frozen cellular environments.

Visiting Scientist, Ritsu Kamiya, University of Tokyo I used electron microscopy to characterize a mutant strain isolated in my graduate studies.

Graduate Student, Wallace Marshall, UC San Francisco I studied the relationship between intraflagellar transport and flagellar length control.

Research Associate, Carolyn Larabell, Lawrence Berkeley National Laboratory I studied cellular defense mechanisms during the early stages of breast cancer metastasis.

Student Intern, Advanced Light Source, Lawrence Berkeley National Laboratory

Ph.D. Cell Biology

1999 -2003
B.A. Molecular and Cell Biology

DFG Grant FOR2092: Biogenesis of Thylakoid Membranes, MPI of Biochemistry

Junior Research Award, MPI of Biochemistry

Alexander von Humboldt Foundation Research Fellowship, MPI of Biochemistry

NSF East Asia and Pacific Summer Institutes (EAPSI) Fellowship, University of Tokyo

Genentech Graduate Fellowship, UC San Francisco

Departmental Honors, Molecular and Cell Biology, UC Berkeley

Supervisor, graduate students Sahradha Albert, Tilak Gupta, Hugo van den Hoek, Luis Kuhn Cuellar, and Chia-Wei Lee; and postdocs Wojciech Wietrzynski and Anna Rast

May 2019
Instructor, Advanced Workshop on Cryo-Electron Tomography; Vienna, Austria

Research Mentor and Classroom Teacher, UC San Francisco Science and Education Partnership

DFG – Forschungsgruppe FOR2092


Dr. Manon Demulder


PhD in Sciences and Bio-Engineering Sciences at Vrije Universiteit Brussel and Ghent University
Focus: Investigate how algae efficiently perform photosynthesis in the phase separating pyrenoid organelle
Doctoral Thesis: “Structure-Function relationship of the Arabidopsis thaliana SOG1, a master regulator in plant DNA damage response"
Hobbies: I am usually busy reading, running or boxing. Nowadays, I often go hiking or biking in or near Munich 

Dr. Ricardo Righetto


PhD in Structural Biology, Biozentrum, University of Basel, Switzerland
Focus: Computational methods development for cryo-electron tomography
Doctoral Thesis: "Single Particle 2D Electron Crystallography for Membrane Protein Structure Determination"
Hobbies: I enjoy outdoor activities such as hiking and biking, and also going to museums and music concerts.

Dr. Florent Waltz


PhD in Molecular and Cellular Biology, University of Strasbourg, France
Focus: Investigation of the structural and functional diversity of the main mitochondrial molecular complexes
Doctoral Thesis: "Characterization of the mitochondrial translation apparatus of Arabidopsis thaliana"
Hobbies: I enjoy travelling the world to discover new cultures and food! 

Dr. Wojciech Wietrzynski ​


PhD Student

Hugo van den Hoek


Lorenz Lamm

MSc in Mathematics, Technical University München
Focus: Machine Learning and Deep Learning
Master Thesis: "Developing a Deep Learning-aided pipeline for detection of membrane bound proteins in cryo-electron tomograms"
Hobbies: On a sunny day, you can find me on the beach volleyball court, hiking in the mountains or just taking a break at the Isar.

Selected Publications

Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity

Tilak Kumar Gupta, Sven Klumpe, Karin Gries, (...), Benjamin D Engel, Cell. 2021 Jul 8;184(14):3643-3659.e23. doi: 10.1016/j.cell.2021.05.011. Epub 2021 Jun 23.

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Charting the native architecture of Chlamydomonas thylakoid membranes with single-molecule precision

Wojciech Wietrzynski, Miroslava Schaffer, Dimitry Tegunov, Sahradha Albert, Atsuko Kanazaw,Jürgen M Plitzko, Wolfgang Baumeister Benjamin D Engel, Elife. 2020 Apr 16;9:e53740. doi: 10.7554/eLife.53740.

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VIPP2 Interacts With VIPP1 and HSP22E/F at Chloroplast Membranes and Modulates a Retrograde Signal for HSP22E/F Gene Expression

Theis J, Niemeyer J  ,Schmollinger S , Ries F , Rütgers M  Gupta TK , Sommer F , Muranaka LS , Venn B , Schulz-Raffelt M , Willmund F , Engel BD , Schroda M 

Plant Cell Environ​​​​​​ doi: 10.1111/pce.13732.

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Direct Visualization of Degradation Microcompartments at the ER Membrane

Albert S, Wietrzynski W , Lee C , Schaffer M, Beck, F , Schuller JM , Salomé PA, Plitzko JM, Baumeister W, Engel BD

Proc Natl Acad Sci U S A 117 (2), 1069-1080

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A Helical Inner Scaffold Provides a Structural Basis for Centriole Cohesion

Le Guennec M, Klena N, Gambarotto D, Laporte MH, Tassin A , van den Hoek H, Erdmann PS, Schaffer M, Kovacik L, Borgers S,Goldie KN, Stahlberg H, Bornens M,  Azimzadeh J, Engel BD, Hamel V, Guichard P

Sci Adv, 6 (7), eaaz4137, 2020 Feb 14

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Biogenic regions of cyanobacterial thylakoids form contact sites with the plasma membrane.

Rast A, Schaffer M, Albert S, Wan W, Pfeffer S, Beck F, Plitzko JM, Nickelsen J, Engel BD* (2019). Nature Plants. 5: 436-446.

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Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer

Schuller JM, Birrell JA, Tanaka H, Konuma T, Wulfhorst H, Cox N, Schuller SK, Thiemann J, Lubitz W, Sétif P, Ikegami T, Engel BD, Kurisu G, Nowaczyk MM (2019). Science. 363:257-260.

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Structure of the membrane-assembled retromer coat by cryo-electron tomography

Kovtun O, Leneva N, Bykov YS, Ariotti N, Teasdale RD, Schaffer M, Engel BD, Owen DJ, Briggs JAB, Collins BM (2018). Nature. 561: 561-564.

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mTORC1 controls phase separation and the biophysical properties of the cytoplasm by tuning crowding

Delarue M, Brittingham GP, Pfeffer S, Surovtsev IV, Pinglay S, Kennedy KJ, Schaffer M, Gutierrez JI, Sang D, Poterewicz G, Chung JK, Plitzko JM, Groves JT, Jacobs-Wagner C, Engel BD*, Holt LJ (2018).  Cell. 174: 338-349.e320.

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In situ architecture of the algal nuclear pore complex

Mosalaganti S, Kosinski J, Albert S, Schaffer M, Strenkert D, Salomé PA, Merchant SS, Plitzko JM, Baumeister W, Engel BD*, Beck M (2018). Nature Communications. 9: 2361

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Proteasomes tether to two distinct sites at the nuclear pore complex

Albert S, Schaffer M, Beck F, Mosalaganti S, Asano S, Thomas HF, Plitzko JM, Beck M, Baumeister W, Engel BD* (2017). Proceedings of the National Academy of Sciences USA. 114: 13726-13731

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The structure of the COPI coat determined within the cell

Bykov YS, Schaffer M, Dodonova SO, Albert S, Plitzko JM, Baumeister W, Engel BD*, Briggs JAG (2017). eLife. 6: e32493.

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The Eukaryotic CO2-Concentrating Organelle Is Liquid-like and Exhibits Dynamic

Freeman Rosenzweig ES, Xu B, Kuhn Cuellar L, Martinez-Sanchez A, Schaffer M, Strauss M, Cartwright HN, Ronceray P, Plitzko JM, Förster F, Wingreen NS, Engel BD*, Mackinder LCM, Jonikas MC (2017). Cell. 171: 148-162.e19.

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Dissecting the molecular organization of the translocon-associated protein complex.

Pfeffer S, Dudek J, Schaffer M, Ng BG, Albert S, Plitzko JM, Baumeister W, Zimmermann R, Freeze HH, Engel BD*, Förster F (2017).Nature Communications. 8: 14516.

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In situ structural analysis of Golgi intracisternal protein arrays.

Engel BD*, Schaffer M, Albert S, Asano S, Plitzko JM, Baumeister W (2015). Proceedings of the National Academy of Sciences USA. 112: 11264-11269.

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Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography.

Engel BD*, Schaffer M, Cuellar LK, Villa E, Plitzko JM, Baumeister W (2015). eLife. 4: e04889.

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Helmholtz Pioneer Campus
Helmholtz Zentrum München
Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)

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