PDBsum entry 1ysh

Structural protein/RNA

PDB id: 1ysh

Contents

Protein chains

104 a.a. *

73 a.a. *

84 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

1ysh

Name:

Structural protein/RNA

Title:

Localization and dynamic behavior of ribosomal protein l30e

Structure:

RNA (28-mer). Chain: a. Engineered: yes. RNA (34-mer). Chain: f. Engineered: yes. RNA (101-mer). Chain: b. Engineered: yes.

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Triticum aestivum. Bread wheat. Organism_taxid: 4565. Oryza sativa. Rice. Organism_taxid: 4530.

Biol. unit:

Hexamer (from PQS)

Authors:

M.Halic,T.Becker,J.Frank,C.M.Spahn,R.Beckmann

Key ref:

M.Halic et al. (2005). Localization and dynamic behavior of ribosomal protein L30e. Nat Struct Mol Biol, 12, 467-468. PubMed id: 15864315 DOI: 10.1038/nsmb933

Date:

08-Feb-05 Release date: 05-Jul-05

Protein chain

Q5I7K9  (RL30_WHEAT) -  Large ribosomal subunit protein eL30 from Triticum aestivum

Seq: 112 a.a.

Struc: 104 a.a.*

Protein chain

P0DKK1  (RL371_ORYSJ) -  Large ribosomal subunit protein eL43z from Oryza sativa subsp. japonica

Seq: 92 a.a.

Struc: 73 a.a.

Protein chain

Q69UI2  (RS131_ORYSJ) -  Small ribosomal subunit protein uS15z from Oryza sativa subsp. japonica

Seq: 151 a.a.

Struc: 84 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

G-A-U-G-A-A-G-C-G-U-G-C-C-G-A-A-A-G-G-C-A-C-G-U-G-G-A-A 28 bases

C-A-A-C-U-C-C-G-U-G-G-A-A-G-C-C-G-U-A-A-U-G-G-C-A-G-G-A-A-G-C-G-G-A 34 bases

U-A-G-A-C-G-G-U-G-G-G-A-G-A-G-G-G-U-G-G-U-G-G-A-A-U-U-C-C-C-G-G-A-G-U-A-G-C-G- 101 bases

DOI no: 10.1038/nsmb933

Nat Struct Mol Biol 12:467-468 (2005)

PubMed id: 15864315

Localization and dynamic behavior of ribosomal protein L30e.

M.Halic, T.Becker, J.Frank, C.M.Spahn, R.Beckmann.

ABSTRACT

The ribosomal protein L30e is an indispensable component of the eukaryotic 80S ribosome, where it is part of the large (60S) ribosomal subunit. Here, we determined the localization of L30e in the cryo-EM map of the 80S wheat germ (wg) ribosome at a resolution of 9.5 A. L30e is part of the interface between large and small subunits, where it dynamically participates in the formation of the two intersubunit bridges eB9 and B4.

Selected figure(s)

Figure 1.
Figure 1. Localization of L30e in a 9.5-Å cryo-EM map of the 80S ribosome. (a) Cryo-EM density of the wheat germ 80S ribosome (accession code EMD-3361 in EMBL 3D-EM database). Yellow, 40S subunit; blue, 60S subunit; green, P-site tRNA; magenta, L30e; SB, stalk base; CP, central protuberance. Right density is rotated by 150°. (b) L30e as part of the isolated 60S subunit density. SRL, sarcin ricin loop. (c) 25S RNA secondary structure diagram of domains II and III. Magenta, L30e-binding region of helix 58 (R.R. Gutell, University of Texas at Austin, http://www.rna.icmb.utexas.edu).

Figure 2.
Figure 2. Model of L30e in its ribosomal environment. (a) Wheat germ L30e amino acid sequence with cylinders and arrows indicating -helical and -strand secondary structure, respectively. (b) Top, L30e density at different contour levels (2.5 and 1 ). Bottom, adjusted homology model of L30e in transparent EM density and L30e crystal structure (green, PDB entry, chain D1NMUD). Note the different conformation of 4. (c) Ribosomal environment of L30e (accession code 1YSH in the Protein Data Bank). Blue, 25S RNA; orange, L37Ae and unknown protein cluster II; magenta, L30e; yellow, 18S RNA; green, S13e (S15p). Ribosome indicates orientation. (d) L30e conformation in the post state and in the eEF2-bound state of the 80S ribosome. The same region of the 60S subunit is shown in the post state (left, wg ribosome, filtered to 13) and in the eEF2-bound state (right, yeast ribosome at 12). B4 and eB9 indicate intersubunit bridges. Note the differences in the density for 4 of L30e (magenta).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2005, 12, 467-468) copyright 2005.