PDBsum entry 1trj

Signaling protein

PDB id: 1trj

Contents

Protein chain

314 a.a.* *

DNA/RNA

* Residue conservation analysis

* C-alpha coords only

PDB id:

1trj

Name:

Signaling protein

Title:

Homology model of yeast rack1 protein fitted into 11.7a cryo-em map of yeast 80s ribosome

Structure:

Helix 39 of 18s rrna. Chain: b. Engineered: yes. Helix 40 of 18s rrna. Chain: c. Engineered: yes. Guanine nucleotide-binding protein beta subunit-like protein. Chain: a.

Source:

Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932

Authors:

J.Sengupta,J.Nilsson,R.Gursky,C.M.Spahn,P.Nissen,J.Frank

Key ref:

J.Sengupta et al. (2004). Identification of the versatile scaffold protein RACK1 on the eukaryotic ribosome by cryo-EM. Nat Struct Mol Biol, 11, 957-962. PubMed id: 15334071 DOI: 10.1038/nsmb822

Date:

21-Jun-04 Release date: 28-Sep-04

Protein chain

P38011  (GBLP_YEAST) -  Small ribosomal subunit protein RACK1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 319 a.a.

Struc: 314 a.a.

DNA/RNA chains

C-C-G-C-C-G-U-U-A-G-U-U-G-C-C-A-G-C-G-G-U-U-C-G-G-C-C-G-G-G-C-A-C-U-C-U-A-A-C- 41 bases

G-A-C-U-G-C-C-C-G-C-G-A-A-A-G-C-G-G-G-A-G-G-A-A-G-G-A 27 bases

Key reference

DOI no: 10.1038/nsmb822

Nat Struct Mol Biol 11:957-962 (2004)

PubMed id: 15334071

Identification of the versatile scaffold protein RACK1 on the eukaryotic ribosome by cryo-EM.

J.Sengupta, J.Nilsson, R.Gursky, C.M.Spahn, P.Nissen, J.Frank.

ABSTRACT

RACK1 serves as a scaffold protein for a wide range of kinases and membrane-bound receptors. It is a WD-repeat family protein and is predicted to have a beta-propeller architecture with seven blades like a Gbeta protein. Mass spectrometry studies have identified its association with the small subunit of eukaryotic ribosomes and, most recently, it has been shown to regulate initiation by recruiting protein kinase C to the 40S subunit. Here we present the results of a cryo-EM study of the 80S ribosome that positively locate RACK1 on the head region of the 40S subunit, in the immediate vicinity of the mRNA exit channel. One face of RACK1 exposes the WD-repeats as a platform for interactions with kinases and receptors. Using this platform, RACK1 can recruit other proteins to the ribosome.

Selected figure(s)

Figure 3.
Figure 3. Ribosomal binding site for RACK1. (a) View of the anchoring region of RACK1 (red) showing interactions with the 18S rRNA helices 39 and 40. (b) View of RACK1 and protein neighbors, rpS3 (S3p), rpS5 (S7p), rpS16 (S9p) and rpS20 (S10p) from the 40S subunit head region (corresponding ribosomal proteins in E. coli are indicated in parentheses). Thumbnails to the right of each panel represent 40S subunit structure in the corresponding views to aid orientation. Atomic coordinates for small subunit proteins and 18S rRNA were taken from PDB entry 1S1H23, and all representations were made using Ribbons44. Landmarks of the 40S subunit: bk, beak; pt, platform.

Figure 5.
Figure 5. Src interaction site on the ribosome. (a) The approximate position of Src-interacting residues on the 80S ribosome relative to the mRNA path (red) and P-site tRNA (green). (b) Ribbon representation of the RACK1 homology model in the same orientation as in a with the two Src-interacting residues indicated.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 957-962) copyright 2004.

Figures were selected by an automated process.