Martin Pilhofer: Catalogue data in Spring Semester 2019

Name Prof. Dr. Martin Pilhofer
FieldCryo-Electron Microscopy
Inst. f. Molekularbiol.u.Biophysik
ETH Zürich, HPK F 13
Otto-Stern-Weg 5
8093 Zürich
Telephone+41 44 633 39 63
RelationshipAssociate Professor

551-0307-01LMolecular and Structural Biology II: From Gene to Protein
D-BIOL students are obliged to take part I and part II as a two-semester course.
3 credits2VN. Ban, F. Allain, S. Jonas, M. Pilhofer
AbstractThis course will cover advanced topics in molecular biology and biochemistry with emphasis on the structure and function of cellular assemblies involved in expression and maintenance of genetic information. We will cover the architecture and the function of molecules involved in DNA replication, transcription, translation, nucleic acid packaging in viruses, RNA processing, and CRISPER/CAS system.
ObjectiveStudents will gain a deep understanding of large cellular assemblies and the structure-function relationships governing their function in fundamental cellular processes ranging from DNA replication, transcription and translation. The lectures throughout the course will be complemented by exercises and discussions of original research examples to provide students with a deeper understanding of the subjects and to encourage active student participation.
ContentAdvanced class covering the state of the research in structural molecular biology of basic cellular processes with emphasis on the function of large cellular assemblies.
Lecture notesUpdated handouts will be provided during the class.
LiteratureThe lecture will be based on the latest literature. Additional suggested
Branden, C., and J. Tooze, Introduction to Protein Structure, 2nd ed.
(1995). Garland, New York.
551-1405-00LElectron Cryomicroscopy Seminar0 credits0.5SM. Pilhofer, further lecturers
AbstractIntergroup seminar for scientists and students interested in electron cryomicroscopy
ObjectiveThe goal of the seminar is to provide an exchange forum for anyone interested in electron cryomicroscopy (tomography and single particle).
The first ~10 minutes are used for exchange on instrument status and technical issues, followed by a ~30 min presentation and discussion of a specific project.
The seminar can also be used to discuss current literature and report from conferences.
Prerequisites / NoticePresented project data are confidential. Sign-up for seminar announcements by emailing
551-1412-00LMolecular and Structural Biology IV: Visualizing Macromolecules by X-Ray Crystallography and EM4 credits2VN. Ban, D. Böhringer, T. Ishikawa, M. A. Leibundgut, K. Locher, M. Pilhofer, K. Wüthrich, further lecturers
AbstractThis course provides an in-depth discussion of two main methods to determine the 3D structures of macromolecules and complexes at high resolution: X-ray crystallography and cryo-electron microscopy. Both techniques result in electron density maps that are interpreted by atomic models.
ObjectiveStudents will obtain the theoretical background to understand structure determination techniques employed in X-ray crystallography and electron microscopy, including diffraction theory, crystal growth and analysis, reciprocal space calculations, interpretation of electron density, structure building and refinement as well as validation. The course will also provide an introduction into the use of cryo-electron tomography to visualize complex cellular substructures at sub-nanometer resolutions, effectively bridging the resolution gap between optical microscopy and single particle cryo-electron microscopy. Lectures will be complemented with practical sessions where students will have a chance to gain hands on experience with sample preparation, data processing and structure building and refinement.
ContentFebruary 22 Lecture 1 Prof. Dr. Kurt Wüthrich
History of Structural Molecular Biology

March 1 Lecture 2 Prof. Dr. Kaspar Locher
X-ray diffraction from macromolecular crystals

March 8 Lecture 3 Prof. Dr. Kaspar Locher
Data collection and statistics, phasing methods

March 15 Lecture 4 Prof. Dr. Nenad Ban
Crystal symmetry and space groups

March 22 Lecture 5 Ban Lab
Practical session with X-ray data processing

March 29 Lecture 6 Prof. Dr. Takashi Ishikawa
Principle of cryo-EM for biological macromolecules I, including hardware of TEM and detectors, image formation principle (phase contrast, spherical aberration, CTF), 3D reconstruction (central-section theorem, backprojection, missing information)

April 5 Lecture 7 Dr. Daniel Boehringer
Single particle analysis, including principle (projection matching, random conical tilt, angular reconstitution)

April 12 Lecture 8 Ban Lab
Practical session including specimen preparation (cryo, negative stain, visit to ScopeM

May 3 Lecture 9
Prof. Dr. M. Pilhofer
Tomography I, including basics and subtomogram averaging

May 10 Lecture 10 Ban Lab
Practical session with example initial EM data processing

May 17 Lecture 11 Prof. Dr. Martin Pilhofer
Practical session (including recent techniques, including cryo-FIB)

May 24 Lecture 12 Prof. Dr. Nenad Ban
EM and X-ray structure building, refinement, validation and interpretation

May 31 Lecture 13 Ban Lab
Practical session with model building and refinemen