PDBsum entry 1ck2

Ribosome

PDB id: 1ck2

Contents

Protein chain

104 a.a. *

* Residue conservation analysis

PDB id:

1ck2

Name:

Ribosome

Title:

Yeast (saccharomyces cerevisiae) ribosomal protein l30

Structure:

60s ribosomal protein l30. Chain: a. Synonym: rl30_yeast. Engineered: yes. Other_details: this entry, 1ck2, is the replacement of 1cn6 cited in the primary reference

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organelle: ribosome, 60s subunit. Cellular_location: cytoplasm. Gene: rpl30. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Other_details: recombinant expression as a c-terminal maltose-

NMR struc:

1 models

Authors:

H.Mao,J.R.Willamson

Key ref:

H.Mao and J.R.Williamson (1999). Local folding coupled to RNA binding in the yeast ribosomal protein L30. J Mol Biol, 292, 345-359. PubMed id: 10493880 DOI: 10.1006/jmbi.1999.3044

Date:

26-Apr-99 Release date: 14-Oct-99

Protein chain

P14120  (RL30_YEAST) -  Large ribosomal subunit protein eL30 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 105 a.a.

Struc: 104 a.a.

DOI no: 10.1006/jmbi.1999.3044

J Mol Biol 292:345-359 (1999)

PubMed id: 10493880

Local folding coupled to RNA binding in the yeast ribosomal protein L30.

H.Mao, J.R.Williamson.

ABSTRACT

The ribosomal protein L30 from yeast Saccharomyces cerevisiae auto-regulates its own synthesis by binding to a structural element in both its pre-mRNA and its mRNA. The three-dimensional structures of L30 in the free (f L30) and the pre-mRNA bound (b L30) forms have been solved by nuclear magnetic resonance spectroscopy. Both protein structures contain four alternating alpha-helices and four beta-strands segments and adopt an overall topology that is an alphabetaalpha three-layer sandwich, representing a unique fold. Three loops on one end of the alphabetaalpha sandwich have been mapped as the RNA binding site on the basis of structural comparison, chemical shift perturbation and the inter-molecular nuclear Overhauser effects to the RNA. The structural and dynamic comparison of f L30 and b L30 reveals that local dynamics may play an important role in the RNA binding. The fourth helix in b L30 is longer than in f L30, and is stabilized by RNA binding. The exposed hydrophobic surface that is buried upon RNA binding may provide the energy necessary to drive secondary structure formation, and may account for the increased stability of b L30.

Selected figure(s)

Figure 6.
Figure 6. Schematic representations of the structures of fL30 (upper panel) and bL30 (lower panel). (a) and (c) Show the stereoviews of a best-fit backbone superposition of the 21 simulated annealing structures of fL30 and bL30, respectively. Only backbone atoms (N, Ca, C') are shown. The coloring schemes are as follows: Ala2 to Ser20, Gly72 to Gly88, and Glu94 to Ala55 in green, Gly21 to Gly26, Leu41 to Ala46, Lys66 to Gln71, and Val89 to Leu93 are in magenta, and Tyr27 to Lys40 and Asn47 to Thr65 are in cyan. (b) and (d) Show the ribbon diagrams of the respective fL30 and bL30 average structures, depicting the secondary structural elements with the corresponding labeled. The regular secondary structures are colored in green (a1 and a4), magenta (b-sheet), and cyan (a2 and a3), and the loop regions are colored in white. The ribbon diagrams were generated with RIBBONS (Carson, 1987).

Figure 10.
Figure 10. Schematic representation of the topologies of two basic abc/ad-units (A) and (B), and the abc/ad- unit in L30. Segments a, b, c, and d are highlighted in red, green, yellow and cyan, respectively. The topology of L30 is a variant of (B), with a long loop (in pink) inserted between the a (in red) and b (in green) seg- ments. For clarification, the L30 is labeled with its sec- ondary segments (i.e. a2, b1).

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 292, 345-359) copyright 1999.

Figures were selected by the author.

Author's comment

The flexible region (residues 74-88) in L30e becomes ordered upon binding to RNA. In this NMR structure, there are few NOEs that define the flexible region. This region adopts two distinct secondary structures in the X-ray structure of the free protein (PDB entry 1nmu), one of which is preferentially bound in the RNA protein complex (PDB entry 1t0k).
James R. Williamson