Molecular Visualization Exercises For Modules 1-3.
Module 1: Size and Components of Cells and Implications with respect to Regulation
View the following structure from the PDB Web site:
M. Tuberculosis Enoyl-Acp Reductase (Inha) In Complex With Nad+ and C16-Fatty-Acyl-Substrate (1bvr)
Module 2: Fatty Acid Synthases (FAS), Polyketide Synthases (PKS), and Non-ribosomal Polypeptide Synthases (NRPS)
View the following structures from the PDB Web site:
B-Ketoacyl-[Acyl Carrier Protein] Synthase I In Complex With Thiolactomycin (1FJ4)
B-Ketoacyl-[Acyl Carrier Protein] Synthase I In Complex With Cerulenin (1FJ8)
In conjunction with viewing the structures, refer to the following paper:
Price, A. C. et al. "Inhibition of B-Ketoacyl-Acyl Carrier Protein Synthases by Thiolactomycin and Cerulenin." J. Biol. Chem. 276 (2001): 6551-9.
Module 3: Translation: Loading, Initiation, Elongation, and Termination - A Machine in Action; Introduction to G-proteins: Switches or Motors
Download the appropriate version of Rasmol from this Web site.
Next download each script file and pdb file in the following table and save them all in the same folder as you have saved Rasmol. Then in the Rasmol command line type:
script <spt file name>
The file should open and the command line window should display information about the structure and coloring which is also given in the table below.
| IMAGE DESCRIPTION | SPT FILES | PDB FILES |
|---|---|---|
| EF-Tu and GDPNP and tRNA | 1ttt (SPT) | 1ttt (PDB) |
| EF-Tu and GDP (P loop is magenta, switch 1 is green, switch 2 is blue, domain 2 is red, domain 3 is magenta) | 1tui (SPT) | 1tui (PDB) |
| Editing domain in red, active site in green, conserved residues HIGH 64-67 in magenta, KMSKS 545-548 in yellow | 1ile (SPT) | 1ile (PDB) |
| IleRS with 3' end folded into active site | 1gtr (SPT) | 1gtr (PDB) |
| IleRS with pseudomonic acid | 1qu2 (SPT) | 1qu2 (PDB) |
Structure References
Ban, N., P. Nissen, J. Hansen, P. B. Moore, and T. A. Steitz. "The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution." Science 289 (2000): 905-20. (H. marismortui)
Yusupov, M. M., G. Z. Yusupova, A. Baucom, K. Lieberman, T. N. Earnest, J. H. Cate, and H. F. Noller. "Crystal Structure of the Ribosome at 5.5 Å Resolution." Science 292 (2001): 883-96. (T. thermophilus)
Wimberly, B. T., D. E. Brodersen, W. M. Clemons, Jr., R. J. Morgan-Warren, A. P. Carter, C. Vonrhein, T. Hartsch, and V. Ramakrishnan. "Structure of the 30S Ribosomal Subunit." Nature 407 (2000): 327-39.
Carter, A. P., W. M. Clemons, D. E. Brodersen, R. J. Morgan-Warren, B. T. Wimberly, and V. Ramakrishnan. "Functional Insights from the Structure of the 30S Ribosomal Subunit and Its Interactions with Antibiotics." Nature 407 (2000): 340-8.
Schlunzen F., R. Zarivach, J. Harms, A. Bashan, A. Tocilj, R. Albrecht, A. Yonath, and F. Franceschi. "Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Centre in Eubacteria." Nature 413 (2001): 814-21. (D. radiodurans)
Steitz, T. A., and P. B. Moore. "RNA, the First Macromolecular Catalyst: The Ribosome is a Ribozyme." TIBS 28, no. 8 (2003): 411-418. (50S structure)