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.

Running the IMP/PMI scripts:

• 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.

Information

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.