PDBsum entry 1k5y

Ribosome

PDB id

1k5y

Contents

			Protein chains

					213 a.a.*


					244 a.a.*


					359 a.a.*


					256 a.a.*


					222 a.a.*


					161 a.a.*


					119 a.a.*


					178 a.a.*


					165 a.a.*


					165 a.a.*


					131 a.a.*


					194 a.a.*


					146 a.a.*


					147 a.a.*


					120 a.a.*


					141 a.a.*


					97 a.a.*


					131 a.a.*


					53 a.a.*


					77 a.a.*


					115 a.a.*


					143 a.a.*


					78 a.a.*


					109 a.a.*


					59 a.a.*


					52 a.a.*


					91 a.a.*


					73 a.a.*

			DNA/RNA

* C-alpha coords only

References listed in PDB file

Key reference

Title

Structure of the 80s ribosome from saccharomyces cerevisiae--Trna-Ribosome and subunit-Subunit interactions.

Authors

C.M.Spahn, R.Beckmann, N.Eswar, P.A.Penczek, A.Sali, G.Blobel, J.Frank.

Ref.

Cell, 2001, 107, 373-386. [DOI no: 10.1016/S0092-8674(01)00539-6]

PubMed id

11701127

Abstract

A cryo-EM reconstruction of the translating yeast 80S ribosome was analyzed. Computationally separated rRNA and protein densities were used for docking of appropriately modified rRNA models and homology models of yeast ribosomal proteins. The core of the ribosome shows a remarkable degree of conservation. However, some significant differences in functionally important regions and dramatic changes in the periphery due to expansion segments and additional ribosomal proteins are evident. As in the bacterial ribosome, bridges between the subunits are mainly formed by RNA contacts. Four new bridges are present at the periphery. The position of the P site tRNA coincides precisely with its prokaryotic counterpart, with mainly rRNA contributing to its molecular environment. This analysis presents an exhaustive inventory of an eukaryotic ribosome at the molecular level.



	Figure 2. Figure 2. rRNA Secondary Structure DiagramsSecondary structure diagrams of the 18S rRNA (a) and the 5.8/25S rRNA (b) of S. cerevisiae (http://www.rna.icmb.utexas.edu). Expansion segments in the rRNAs are indicated, using the nomenclature of Gerbi (1996)		Figure 6. Figure 6. Position of the Intersubunit BridgesThe 40S subunit in yellow (a) and the 60S subunit in blue (b) are shown from their intersubunit sides. The intersubunit bridges are shown in red and are annotated with their numbers. Bridges also observed in prokaryotic ribosomes are numbered B1–B7. Additional intersubunit connections in the yeast ribosome are named eB8–eB11 (see also Table 1)

	Headers