PDBsum entry: 1hnw

Ribosome

PDB id: 1hnw

Contents

Protein chains

234 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. *

119 a.a. *

124 a.a. *

125 a.a. *

60 a.a. *

88 a.a. *

88 a.a. *

104 a.a. *

73 a.a. *

80 a.a. *

99 a.a. *

24 a.a. *

DNA/RNA

Ligands

TAC ×2

Metals

_MG ×96

_ZN ×2

* Residue conservation analysis

PDB id:

1hnw

Name:

Ribosome

Title:

Structure of the thermus thermophilus 30s ribosomal subunit in complex with tetracycline

Structure:

16s ribosomal RNA. Chain: a. Fragment of messenger RNA. Chain: x. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4.

Source:

Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274

Biol. unit:

22mer (from PQS)

Resolution:

3.40Å R-factor: 0.222 R-free: 0.264

Authors:

D.E.Brodersen,W.M.Clemons Jr.,A.P.Carter,R.Morgan-Warren, B.T.Wimberly,V.Ramakrishnan

Key ref:

D.E.Brodersen et al. (2000). The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit. Cell, 103, 1143-1154. PubMed id: 11163189 DOI: 10.1016/S0092-8674(00)00216-6

Date:

08-Dec-00 Release date: 21-Feb-01

Protein chain

P80371  (RS2_THET8) -  30S ribosomal protein S2

Seq: 256 a.a.

Struc: 234 a.a.

Protein chain

P80372  (RS3_THET8) -  30S ribosomal protein S3

Seq: 239 a.a.

Struc: 206 a.a.

Protein chain

P80373  (RS4_THET8) -  30S ribosomal protein S4

Seq: 209 a.a.

Struc: 208 a.a.

Protein chain

Q5SHQ5  (RS5_THET8) -  30S ribosomal protein S5

Seq: 162 a.a.

Struc: 150 a.a.

Protein chain

Q5SLP8  (RS6_THET8) -  30S ribosomal protein S6

Seq: 101 a.a.

Struc: 101 a.a.

Protein chain

P17291  (RS7_THET8) -  30S ribosomal protein S7

Seq: 156 a.a.

Struc: 155 a.a.

Protein chain

Q5SHQ2  (RS8_THET8) -  30S ribosomal protein S8

Seq: 138 a.a.

Struc: 138 a.a.

Protein chain

P80374  (RS9_THET8) -  30S ribosomal protein S9

Seq: 128 a.a.

Struc: 127 a.a.*

Protein chain

Q5SHN7  (RS10_THET8) -  30S ribosomal protein S10

Seq: 105 a.a.

Struc: 98 a.a.

Protein chain

P80376  (RS11_THET8) -  30S ribosomal protein S11

Seq: 129 a.a.

Struc: 119 a.a.

Protein chain

Q5SHN3  (RS12_THET8) -  30S ribosomal protein S12

Seq: 132 a.a.

Struc: 124 a.a.

Protein chain

P80377  (RS13_THET8) -  30S ribosomal protein S13

Seq: 126 a.a.

Struc: 125 a.a.

Protein chain

Q5SHQ1  (RS14Z_THET8) -  30S ribosomal protein S14 type Z

Seq: 61 a.a.

Struc: 60 a.a.

Protein chain

Q5SJ76  (RS15_THET8) -  30S ribosomal protein S15

Seq: 89 a.a.

Struc: 88 a.a.

Protein chain

Q5SJH3  (RS16_THET8) -  30S ribosomal protein S16

Seq: 88 a.a.

Struc: 88 a.a.

Protein chain

Q5SHP7  (RS17_THET8) -  30S ribosomal protein S17

Seq: 105 a.a.

Struc: 104 a.a.*

Protein chain

Q5SLQ0  (RS18_THET8) -  30S ribosomal protein S18

Seq: 88 a.a.

Struc: 73 a.a.*

Protein chain

Q5SHP2  (RS19_THET8) -  30S ribosomal protein S19

Seq: 93 a.a.

Struc: 80 a.a.

Protein chain

P80380  (RS20_THET8) -  30S ribosomal protein S20

Seq: 106 a.a.

Struc: 99 a.a.*

Protein chain

Q5SIH3  (RSHX_THET8) -  30S ribosomal protein Thx

Seq: 27 a.a.

Struc: 24 a.a.

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

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (4 terms)
• Biological process: translation (1 term)
• Biochemical function: structural constituent of ribosome (6 terms)

DOI no: 10.1016/S0092-8674(00)00216-6

Cell 103:1143-1154 (2000)

PubMed id: 11163189

The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit.

D.E.Brodersen, W.M.Clemons, A.P.Carter, R.J.Morgan-Warren, B.T.Wimberly, V.Ramakrishnan.

ABSTRACT

We have used the recently determined atomic structure of the 30S ribosomal subunit to determine the structures of its complexes with the antibiotics tetracycline, pactamycin, and hygromycin B. The antibiotics bind to discrete sites on the 30S subunit in a manner consistent with much but not all biochemical data. For each of these antibiotics, interactions with the 30S subunit suggest a mechanism for its effects on ribosome function.

Selected figure(s)

Figure 1.
Figure 1. Overview of Tetracycline, Pactamycin, and Hygromycin B in the 30S SubunitAntibiotics are shown as space-filling models, with tetracycline (blue), pactamycin (green), and hygromycin B (red). The parts of 16S RNA that make contacts with any of the three antibiotics are colored as in the following figures.

Figure 2.
Figure 2. Tetracycline(a) Stereo figure of the primary Tc binding site (A site region) with rings A, B, C, and D of the fused-ring system. H34 (top left, blue) and H31 (top right, green) are shown together with H44 (cyan). The enhanced reactivity of C1054 (green sphere) and the reduced UV cross-link C967xC1400 (dashed red line) are indicated. The bound magnesium ion (gold sphere) is shown with residues involved in its coordination (thick sticks, light blue). The initial difference electron density map (mF[o]-DF[c]), calculated before inclusion of Tc in the model, is shown at 6σ.(b) Overview of primary binding site of Tc indicating the RNA components close to the site and the interaction with A site tRNA, H34 (blue), H31 (green), H18 (orange), and H44 (cyan). The model of A site tRNA (red) and mRNA (yellow) is shown.(c) Chemical structure diagram of Tc and possible interactions with 16S RNA at the primary site (blue). The shaded area represents positions on the molecule that can be modified without affecting its inhibitory action ([31]).(d) Stereo figure of the secondary tetracycline site (H27 switch region) with rings A, B, C, and D. H27 is yellow/green/red and H11 violet. The 885–887:910–912 base pairs are shown in red, whereas the bases 888–890, involved in a proposed alternative base-pairing scheme are green. The reduced reactivity towards DMS at A892 (red sphere) and the reduced cross-link G894-U244 (red dashed line) are also shown. The initial difference electron density map (mF[o]-DF[c]) is shown at 4σ.(e) Overview of secondary binding site of Tc along with the RNA elements it interacts with, H11 (violet), H27 (yellow, red, and green as above).(f) Possible hydrogen bond interactions with 16S RNA at the secondary tetracycline binding site (blue).

The above figures are reprinted by permission from Cell Press: Cell (2000, 103, 1143-1154) copyright 2000.

Figures were selected by the author.