FY2012 Annual Report

Structural Cellular Biology Unit

Professor Ulf Skoglund



Our unit runs research projects that concern method developments, applications, and rewarding and exciting collaborations with other groups in order to understand more of the function of proteins in cells and tissues.  In addition we are also developing basic mathematics to establish a more generalized information theory enabling a more quantitative use of the information in measured data.

We mainly use the techniques of electron microscopy, including molecular electron tomography, as the main tools in our unit, though we will draw upon well-established complementary techniques when called for.

This third year we have been very busy developing experimental protocols for our high-end electron microscopes and continuing developing our software, hiring more coworkers and starting data acquisition in our ongoing structural projects. 

Our method is well suited for use in pharmaceutical drug research in industrial collaborations, so a big leap forward was that we managed to get a MEXT grant that funds a spin-of formation. Currently this spin-off is being created.

1. Staff

  • Dr. Ulf Skoglund, Professor
  • Dr. Lars-Göran Öfverstedt, Researcher
  • Dr. Gunnar Wilken, Researcher
  • Dr. Yumiko Mishima, Researcher
  • Dr. Cahyo Budiman, Researcher (shared with IPB Unit)
  • Mr. Hirotoshi Furusho, Technician
  • Mr. Jakub Kolodziejczyk, Technician
  • Ms. Ruby May Andales, Technician
  • Ms. Shizuka Kuda, Research Administrator

2. Collaborations

  • Theme: Lipid Membrane Ion Channel KcsA, a Potassium ion-channel
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor, Shigetoshi Oiki, University of Fukui
  • Theme: Human Skin Structure
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor Lars Norlen, Karolinska Institutet
  • Theme: Structure and function of Glucocorticoid receptor protein
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor Örjan Wrange, Karolinska Institutet
  • Theme: Structure and function of proteins involved in Malaria infection
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor Mats Wahlgren, Karolinska Institutet
  • Theme: Structure and function of the Ryanodine receptor and its complexes
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor Ichiro Maruyama, OIST
  • Theme: Atomic structure of small nano-particles
    • Type of collaboration: Research Collaboration
    • Researchers:
      • Professor Mukhles Sowwan, OIST

3. Activities and Findings


Our Unit has continued to develop our 3D tomographic software. The latest version, 5.6, is now a stable representation and a version has been also installed at Professor Shigetoshi Oikis lab at University of Fukuji. The Krios cryo-TEM has now been actively used to collect new and very high quality datasets of molecules within our collaborations.  

We managed to show MEXT that we could use our software to successfully finalize a proof-of-concept structural determination-project on a smaller sized protein (about 32 kD) in collaboration with a well-known Japanese pharmaceutical company. This is the smallest individual protein that has been studied in 3D so far.

Our regularization software COMET has also been updated to include local geometry refinement. This is the first time this has been achieved, and we are planning an article on this. This new feature helped in a test case for a another OIST Unit where they wanted to see if our methods could be used in their quest for understanding the atomic structure layout in the synthesized nanoparticles. Our 3D regularized nanoparticle structure clearly show the atomic lattice in large regions of the small nanoparticle.

4. Publications

4.1 Journals

1.         Walser, P. J., Ariotti, N., Howes, M., Ferguson, C., Webb, R., Schwudke, D., Leneva, N., Cho, K. J., Cooper, L., Rae, J., Floetenmeyer, M., Oorschot, V. M. J., Skoglund, U., Simons, K., Hancock, J. F. & Parton, R. G.  Constitutive Formation of Caveolae in a Bacterium. Cell 150, 752-763, doi:10.1016/j.cell.2012.06.042 (2012).

2.         Iwai, I., Han, H. M., den Hollander, L., Svensson, S., Ofverstedt, L. G., Anwar, J., Brewer, J., Bloksgaard, M., Laloeuf, A., Nosek, D., Masich, S., Bagatolli, L. A., Skoglund, U. & Norlen, L.  The Human Skin Barrier Is Organized as Stacked Bilayers of Fully Extended Ceramides with Cholesterol Molecules Associated with the Ceramide Sphingoid Moiety. Journal of Investigative Dermatology 132, 2215-2225, doi:10.1038/jid.2012.43 (2012).

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

1.         Skoglund, U.  3D visualization of individual protein molecules for functional analysis, OIST Internal Seminar (2012).

2.         Skoglund, U.  molecular electron tomography, OIST MEXT visit (2012).

3.         Skoglund, U.  Using Molecular Electron Tomography to analyze macromolecules, OIST (2012).

4.         Skoglund, U.  Enzymes can be seen, OIST Open Campus (2012).

5.         Budiman, C., Furusho, H., Mishima, Y., Öfverstedt, L., Skoglund, U. & Maruyama, I.  In situ visualization of mouse skeletal muscle ryanodine receptor by cryo-electron tomography, in 57th Annual Meeting of Biophysical Society, Pennsylvania Convention Center, Philadelphia, Pennsylvania, USA (2013).

6.         Wilken, G.  Goodstein sequences for prominent ordinals up to the ordinal of Pi^1_1-CA_0, in 3rd Workshop on Proof Theory and Rewriting, Kanazawa, Japan (2012).

7.         Skoglund, U.  3D visualization of individual protein molecules for functional analysis, in Bio Japan, Yokohama (2012).

5. Intellectual Property Rights and Other Specific Achievements

5.1 Patent

  • Provisional patent filed Local Geometry refinement. Filed Feb 2013
  • Provisional patent filed for Extended field iterative reconstruction technique for correlated noise removal. Filed March 2013.

1 patent has been approved:

Iterated Variational Regularization With ComponentWise Regularization.
Inventors: Ozan Öktem, Hans Rullgård, Johan Lagerros, Lars-Göran Öfverstedt, Anders Edin.
Assignee: OIST

5.2 Grant

  • MEXT Grant-Project for Creating New Industries from University (Nov 2012 – Mar 2014)

6. Meetings and Events

6.1 Seminar

  • Date: April 3, 2012
  • Venue: OIST Campus Lab1
  • Speaker: Professor Lars Norlën (Karolinska Institutet)

6.2 Seminar

  • Date: Nov 22, 2012
  • Venue: OIST Campus Lab1
  • Speaker: Dr. Pan Soonsawad (University of California, Davis)

6.3 Seminar

  • Date: March 26, 2013
  • Venue: OIST Campus Lab1
  • Speaker: Professor Sara Sandin (Nanyang Technological University)

6.4 Conference

  • Date: Oct 10-11, 2012
  • Venue: Bio Japan 2012, Yokohama