Sanbonmatsu Team: Models

PDB 4D5Y | EMDB 2810

Cryo-EM of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus IRES

Muhs et al. (2015) Cryo-EM of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus IRES. Molecular Cell 57 (3), 422-432, published February 5, 2015. doi:10.1016/j.molcel.2014.12.016. View PDF »

PDB 4UJE | EMDB 2620

Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement

Budkevich et al. (2014) Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement. Cell 158 (1), 121-131, published July 3, 2014. doi:10.1016/j.cell.2014.04.044. View PDF »

PDB 3JD5 | EMDB 5941

Cryo-EM Structure of the Small Subunit of the Mammalian Mitochondrial Ribosome

Kaushal et al. (2014) Cryo-EM Structure of the Small Subunit of the Mammalian Mitochondrial Ribosome. Proceedings of the National Academy of Sciences 111 (20), 7284-7289, published May 20, 2014. doi:10.1073/pnas.1401657111. View PDF »

PDB 4V5N | EMDB 1799

Head Swivel on the Ribosome Facilitates Translocation Via Intra-Subunit tRNA Hybrid Sites

Ratje et al. (2010) Head Swivel on the Ribosome Facilitates Translocation Via Intra-Subunit tRNA Hybrid Sites. Nature 468 (7324), 713-716, published December 2, 2010. doi:10.1038/nature09547. View PDF »

All-Atom Homology Model of the Escherichia coli 30S Ribosomal Subunit

Tung et al. (2002) All-Atom Homology Model of the Escherichia coli 30S Ribosomal Subunit. Nature Structural & Molecular Biology 9 (10), 750-755, published September 16, 2002. doi:10.1038/nsb841. View PDF »

Ribosome Model 1

Ratje, A.H, Loerke, J, Mikolajka, A, Brünner, M, Hildebrand, P.W, Starosta, A.L, Dönhöfer, A, Connell, S.R, Fucini, P, Mielke, T, Whitford, P.C, Onuchic, J.N, Yu, Y, Sanbonmatsu, K.Y, Hartmann, R.K, Penczek, P.A, Wilson, D.N, and Spahn, C.M. (2010) Head Swivel on the Ribosome Facilitates Translocation by Means of Intra-Subunit tRNA Hybrid Sites. Nature 468 (7324), 713-716, published December 2, 2010.

All-atom model for cryoelectron microscopy maps of TIPRE (a, b) of the 70S–EF-G–GDP–FA complex are shown in mesh form with docked models in ribbon representation: EF-G (red), tRNA (green), 23S/5S rRNA (blue), 50S ribosomal proteins (orange), 16S rRNA (yellow) and the 30S ribosomal proteins (magenta). The maps are shown from the 30S side with the 30S subunit computationally removed (a) and from the 50S side with the 50S subunit computationally removed (b). CP, central protuberance; bk, beak; sp, spur; pt, platform; h, head; b, back; L1 and L7, ribosomal proteins L1 and L7, respectively; H69, helix 69 of 23S rRNA.

Ribosome Model 2

Ratje, A.H, Loerke, J, Mikolajka, A, Brünner, M, Hildebrand, P.W, Starosta, A.L, Dönhöfer, A, Connell, S.R, Fucini, P, Mielke, T, Whitford, P.C, Onuchic, J.N, Yu, Y, Sanbonmatsu, K.Y, Hartmann, R.K, Penczek, P.A, Wilson, D.N, and Spahn, C.M.T. (2010) Head Swivel on the Ribosome Facilitates Translocation by Means of Intra-Subunit tRNA Hybrid Sites. Nature 468 (7324), 713-716, published December 2, 2010.

All-atom model for cryoelectron microscopy maps of TIPOST (c, d) of the 70S–EF-G–GDP–FA complex are shown in mesh form with docked models in ribbon representation: EF-G (red), tRNA (green), 23S/5S rRNA (blue), 50S ribosomal proteins (orange), 16S rRNA (yellow) and the 30S ribosomal proteins (magenta). The maps are shown from the 30S side with the 30S subunit computationally removed (c) and from the 50S side with the 50S subunit computationally removed (d). CP, central protuberance; bk, beak; sp, spur; pt, platform; h, head; b, back; L1 and L7, ribosomal proteins L1 and L7, respectively; H69, helix 69 of 23S rRNA.

Ribosome Model 3

Whitford, P.C, Ahmed, A, Yu, Y, Hennelly, S.P, Tama, F, Spahn, C.M.T, Onuchic, J.N, and Sanbonmatsu, K.Y. (2011) Excited States of Ribosome Translocation Revealed Through Integrative Molecular Modeling. Proceedings of the National Academy of Sciences 108 (47), 18943-18948, published November 11, 2011. doi:10.1073/pnas.1108363108

Suggested models for transient configurations during translocation. Atomic model of the ribosome with tRNA molecules in a A/P*-P/E configuration, fitted to a cryo-EM density where the mRNA has not translocated (TIpre configuration). The A-site tRNA and domain IV of EF-G are not fit to the density. In the cryo-EM construct domain IV can enter the A site because there is no A/A tRNA present. Here, domain IV is not fit, but it is allowed to relax into an accessible low-energy configuration.

Ribosome Model 4

Suggested models for transient configurations during translocation. Atomic model of the ribosome and tRNAs in an A/P-P/E configuration, fitted to a density map in which the mRNA has partially translocated (TIpost). The concomitant displacement of the A-site tRNA and partial mRNA translocation leads to available space for fitting domain IV of EF-G. Therefore, all atoms were fit to the density, except for the A/P tRNA.

Cryo-EM models

The cryo-EM revolution is sweeping structural biology. With the advent of the direct electron detector, cryo-EM (cryogenic electron microscopy) resolution rivals that of X-ray crystallography. We are automating the process of producing atomistic models from 3-D cryo-EM reconstructions.