PDBsum entry 2e5l

Ribosome

PDB id: 2e5l

Contents

Protein chains

222 a.a. *

206 a.a. *

208 a.a. *

150 a.a. *

101 a.a. *

155 a.a. *

138 a.a. *

127 a.a. *

98 a.a. *

115 a.a. *

124 a.a. *

122 a.a. *

60 a.a. *

88 a.a. *

83 a.a. *

104 a.a. *

73 a.a. *

80 a.a. *

99 a.a. *

24 a.a. *

DNA/RNA

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

2e5l

Name:

Ribosome

Title:

A snapshot of the 30s ribosomal subunit capturing mRNA via the shine- dalgarno interaction

Structure:

16s ribosomal RNA. Chain: a. 5'-r( Gp Ap Ap Ap Gp A)-3'. Chain: 1, 2. Engineered: yes. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c.

Source:

Thermus thermophilus. Organism_taxid: 274. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 274

Resolution:

3.30Å R-factor: 0.259 R-free: 0.301

Authors:

T.Kaminishi,D.N.Wilson,C.Takemoto,J.M.Harms,M.Kawazoe,F.Schluenzen, K.Hanawa-Suetsugu,M.Shirouzu,P.Fucini,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

T.Kaminishi et al. (2007). A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction. Structure, 15, 289-297. PubMed id: 17355865 DOI: 10.1016/j.str.2006.12.008

Date:

21-Dec-06 Release date: 15-May-07

Protein chain

P80371  (RS2_THET8) -  Small ribosomal subunit protein uS2 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 256 a.a.

Struc: 222 a.a.

Protein chain

P80372  (RS3_THET8) -  Small ribosomal subunit protein uS3 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 239 a.a.

Struc: 206 a.a.

Protein chain

P80373  (RS4_THET8) -  Small ribosomal subunit protein uS4 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 209 a.a.

Struc: 208 a.a.

Protein chain

Q5SHQ5  (RS5_THET8) -  Small ribosomal subunit protein uS5 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 162 a.a.

Struc: 150 a.a.

Protein chain

Q5SLP8  (RS6_THET8) -  Small ribosomal subunit protein bS6 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 101 a.a.

Struc: 101 a.a.

Protein chain

P17291  (RS7_THET8) -  Small ribosomal subunit protein uS7 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 156 a.a.

Struc: 155 a.a.

Protein chain

P0DOY9  (RS8_THET8) -  Small ribosomal subunit protein uS8 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 138 a.a.

Struc: 138 a.a.

Protein chain

P80374  (RS9_THET8) -  Small ribosomal subunit protein uS9 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 128 a.a.

Struc: 127 a.a.*

Protein chain

Q5SHN7  (RS10_THET8) -  Small ribosomal subunit protein uS10 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 105 a.a.

Struc: 98 a.a.

Protein chain

P80376  (RS11_THET8) -  Small ribosomal subunit protein uS11 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 129 a.a.

Struc: 115 a.a.

Protein chain

Q5SHN3  (RS12_THET8) -  Small ribosomal subunit protein uS12 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 132 a.a.

Struc: 124 a.a.

Protein chain

P80377  (RS13_THET8) -  Small ribosomal subunit protein uS13 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 126 a.a.

Struc: 122 a.a.

Protein chain

P0DOY6  (RS14Z_THET8) -  Small ribosomal subunit protein uS14 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 61 a.a.

Struc: 60 a.a.

Protein chain

Q5SJ76  (RS15_THET8) -  Small ribosomal subunit protein uS15 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 89 a.a.

Struc: 88 a.a.

Protein chain

Q5SJH3  (RS16_THET8) -  Small ribosomal subunit protein bS16 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 88 a.a.

Struc: 83 a.a.

Protein chain

P0DOY7  (RS17_THET8) -  Small ribosomal subunit protein uS17 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 105 a.a.

Struc: 104 a.a.*

Protein chain

Q5SLQ0  (RS18_THET8) -  Small ribosomal subunit protein bS18 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 88 a.a.

Struc: 73 a.a.*

Protein chain

Q5SHP2  (RS19_THET8) -  Small ribosomal subunit protein uS19 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 93 a.a.

Struc: 80 a.a.

Protein chain

P80380  (RS20_THET8) -  Small ribosomal subunit protein bS20 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 106 a.a.

Struc: 99 a.a.*

Protein chain

Q5SIH3  (RSHX_THET8) -  Small ribosomal subunit protein bTHX from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 27 a.a.

Struc: 24 a.a.

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DNA/RNA chains

U-U-G-G-A-G-A-G-U-U-U-G-A-U-C-C-U-G-G-C-U-C-A-G-G-G-U-G-A-A-C-G-C-U-G-G-C-G-G- ... 1517 bases

G-A-A-A-G-A 6 bases

G-A-A-A 4 bases

Enzyme reactions

• Enzyme class: Chains B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V: E.C.?

DOI no: 10.1016/j.str.2006.12.008

Structure 15:289-297 (2007)

PubMed id: 17355865

A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction.

T.Kaminishi, D.N.Wilson, C.Takemoto, J.M.Harms, M.Kawazoe, F.Schluenzen, K.Hanawa-Suetsugu, M.Shirouzu, P.Fucini, S.Yokoyama.

ABSTRACT

In the initiation phase of bacterial translation, the 30S ribosomal subunit captures mRNA in preparation for binding with initiator tRNA. The purine-rich Shine-Dalgarno (SD) sequence, in the 5' untranslated region of the mRNA, anchors the 30S subunit near the start codon, via base pairing with an anti-SD (aSD) sequence at the 3' terminus of 16S rRNA. Here, we present the 3.3 A crystal structure of the Thermus thermophilus 30S subunit bound with an mRNA mimic. The duplex formed by the SD and aSD sequences is snugly docked in a "chamber" between the head and platform domains, demonstrating how the 30S subunit captures and stabilizes the otherwise labile SD helix. This location of the SD helix is suitable for the placement of the start codon AUG in the immediate vicinity of the mRNA channel, in agreement with reported crosslinks between the second position of the start codon and G1530 of 16S rRNA.

Selected figure(s)

Figure 1.
Figure 1. Location of the SD Helix on the 30S Ribosomal Subunit
(A–C) The rRNA and the ribosomal proteins are colored light blue and pale pink, respectively. (A) Front (subunit interface), side (rotated 145° counterclockwise), and back (solvent) views of the 30S subunit, with the SD helix accommodated in a cavity formed between the head (orange) and platform (green) domains. Oligonucleotides (5′-GAAAGA-3′) are colored yellow, and the 3′ end nucleotides of 16S rRNA from A1534, which were clearly identified in the present structure, but were disordered in previous structures, are colored dark blue. (B) Stereo enlargement of the boxed region in the side view of (A). RNA helices from the head (h28 and h37) and platform (h23a and h26) domains are dark orange and dark green, respectively. The ribosomal proteins surrounding the cavity are colored salmon. (C) Stereo view of the SD helix position on the 30S subunit, which is represented as a molecular surface.

Figure 2.
Figure 2. Stereo Representations of the SD Helix in the Chamber on the 30S Subunit
(A) Close-up view. U723 and G1530–A1531 are represented in magenta and cyan, respectively. Other coloring is as in Figure 1A. The chamber defined by h26, U723, G1530–A1531, and S2 is highlighted with a rectangle.
(B) Detailed view of the SD helix. The 2mF[o] − DF[c] map contoured at 1.5σ shows unbiased density for the SD helix (not included in the refinement). The U723 nucleotide (magenta) on h23a of 16S rRNA faces the minor groove near the proximal end of the SD helix. S18 is omitted for clarity.

The above figures are reprinted by permission from Cell Press: Structure (2007, 15, 289-297) copyright 2007.

Figures were selected by an automated process.