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Sven Klumpe

Our lab develops and applies technologies for in situ structural biology to address questions in germline biology with a special interest in transposable elements. Specifically, we use focused ion beam – scanning electron microscopes (FIB-SEM) to produce cellular thin sections at cryogenic temperatures. In conjunction with high-end transmission electron microscopy (TEM), we can generate three dimensional reconstructions of the cellular interior from these thin sections by cryo-electron tomography. This allows us to study biological macromolecules in their native environment, the inside of a cell.

Publications

2025

Klumpe, S., Senti, KA., Beck, F., Sachweh, J., Hampoelz, B., Ronchi, P., Oorschot, V., Brandstetter, M., Yeroslaviz, A., Briggs, JAG., Brennecke, J., Beck, M., Plitzko, JM. (2025)

In-cell structure and snapshots of copia retrotransposons in intact tissue by cryo-ET.

 Cell.

2024

McCafferty, CL., Klumpe, S., Amaro, RE., Kukulski, W., Collinson, L., Engel, BD. (2024)

Integrating cellular electron microscopy with multimodal data to explore biology across space and time.

 Cell. 187(3):563-584
Schiøtz, OH., Kaiser, CJO., Klumpe, S., Morado, DR., Poege, M., Schneider, J., Beck, F., Klebl, DP., Thompson, C., Plitzko, JM. (2024)

Serial Lift-Out: sampling the molecular anatomy of whole organisms.

 Nat Methods. 21(9):1684-1692
Schiøtz, OH., Klumpe, S., Plitzko, JM., Kaiser, CJO. (2024)

Cryo-electron tomography: en route to the molecular anatomy of organisms and tissues.

 Biochem Soc Trans. 52(6):2415-2425

2023

Dumoux, M., Glen, T., Smith, JLR., Ho, EML., Perdigão, LMA., Pennington, A., Klumpe, S., Yee, NBY., Farmer, DA., Lai, PYA., Bowles, W., Kelley, R., Plitzko, JM., Wu, L., Basham, M., Clare, DK., Siebert, CA., Darrow, MC., Naismith, JH., Grange, M. (2023)

Cryo-plasma FIB/SEM volume imaging of biological specimens.

 Elife. 12

2022

Hung, KYS., Klumpe, S., Eisele, MR., Elsasser, S., Tian, G., Sun, S., Moroco, JA., Cheng, TC., Joshi, T., Seibel, T., Van Dalen, D., Feng, XH., Lu, Y., Ovaa, H., Engen, JR., Lee, BH., Rudack, T., Sakata, E., Finley, D. (2022)

Allosteric control of Ubp6 and the proteasome via a bidirectional switch.

 Nat Commun. 13(1):838

2021

Erdmann, PS., Hou, Z., Klumpe, S., Khavnekar, S., Beck, F., Wilfling, F., Plitzko, JM., Baumeister, W. (2021)

In situ cryo-electron tomography reveals gradient organization of ribosome biogenesis in intact nucleoli.

 Nat Commun. 12(1):5364
Gupta, TK., Klumpe, S., Gries, K., Heinz, S., Wietrzynski, W., Ohnishi, N., Niemeyer, J., Spaniol, B., Schaffer, M., Rast, A., Ostermeier, M., Strauss, M., Plitzko, JM., Baumeister, W., Rudack, T., Sakamoto, W., Nickelsen, J., Schuller, JM., Schroda, M., Engel, BD. (2021)

Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity.

 Cell. 184(14):3643-3659.e23
Klumpe, S., Fung, HK., Goetz, SK., Zagoriy, I., Hampoelz, B., Zhang, X., Erdmann, PS., Baumbach, J., Müller, CW., Beck, M., Plitzko, JM., Mahamid, J. (2021)

A modular platform for automated cryo-FIB workflows.

 Elife. 10
Liu, Z., Gao, J., Cui, Y., Klumpe, S., Xiang, Y., Erdmann, PS., Jiang, L. (2021)

Membrane imaging in the plant endomembrane system.

 Plant Physiol. 185(3):562-576
Tacke, S., Erdmann, P., Wang, Z., Klumpe, S., Grange, M., Plitzko, J., Raunser, S. (2021)

A streamlined workflow for automated cryo focused ion beam milling.

 J Struct Biol. 213(3):107743
Zinzula, L., Basquin, J., Bohn, S., Beck, F., Klumpe, S., Pfeifer, G., Nagy, I., Bracher, A., Hartl, FU., Baumeister, W. (2021)

High-resolution structure and biophysical characterization of the nucleocapsid phosphoprotein dimerization domain from the Covid-19 severe acute respiratory syndrome coronavirus 2.

 Biochem Biophys Res Commun. 538:54-62
Zinzula, L., Beck, F., Klumpe, S., Bohn, S., Pfeifer, G., Bollschweiler, D., Nagy, I., Plitzko, JM., Baumeister, W. (2021)

Cryo-EM structure of the cetacean morbillivirus nucleoprotein-RNA complex.

 J Struct Biol. 213(3):107750

2020

Schrepfer, P., Ugur, I., Klumpe, S., Loll, B., Kaila, VRI., Brück, T. (2020)

Exploring the catalytic cascade of cembranoid biosynthesis by combination of genetic engineering and molecular simulations.

 Comput Struct Biotechnol J. 18:1819-1829

2019

Katzmeier, F., Aufinger, L., Dupin, A., Quintero, J., Lenz, M., Bauer, L., Klumpe, S., Sherpa, D., Dürr, B., Honemann, M., Styazhkin, I., Simmel, FC., Heymann, M. (2019)

A low-cost fluorescence reader for in vitro transcription and nucleic acid detection with Cas13a.

 PLoS One. 14(12):e0220091