40S•eIF1•eIF3 Complex

Eukaryotic translation initiation requires the recruitment of the large, multiprotein eIF3 complex to the 40S ribosomal subunit. Using X-ray structures of all major components of the minimal, six-subunit Saccharomyces cerevisiae eIF3 core, together with cross-linking coupled to mass spectrometry, we were able to use IMP to position and orient all eIF3 components on the 40S•eIF1 complex, revealing an extended, modular arrangement of eIF3 subunits.

• cd modeling/template
• ./bigj-ac-40s.modeling.py Only_10_7 cross-links.csv all 4.0 move_ac 0.01 Triple (on a single processor; prepend mpirun -np 4 or similar if you built IMP with MPI support)

The calculation will generate a trajectory, output/rmfs/0.rmf3, in RMF format. For convenience, the 100 best-scoring models are also output in PDB format in the output/pdbs directory.

Author(s): Riccardo Pellarin, Peter Cimermančič

License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Last known good IMP version:

Testable: Yes.

Parallelizeable: Yes

Publications:

• J. Erzberger, F. Stengel, R. Pellarin, S. Zhang, T. Schaefer, C. Aylett, P. Cimermančič, D. Boehringer, A. Sali, R. Aebersold, N. Ban. Molecular architecture of the 40S•eIF1•eIF3 translation initiation complex, Cell 158, 1125-1135, 2014.