PDBsum entry 3knh

Ribosome/antibiotic

PDB id: 3knh

Contents

Protein chains

235 a.a. *

207 a.a. *

208 a.a. *

151 a.a. *

101 a.a. *

155 a.a. *

138 a.a. *

127 a.a. *

99 a.a. *

119 a.a. *

125 a.a. *

120 a.a. *

60 a.a. *

88 a.a. *

84 a.a. *

100 a.a. *

70 a.a. *

79 a.a. *

99 a.a. *

25 a.a. *

DNA/RNA

Ligands

KBE-DPP-SER-SER-UAL-5OH

Metals

_MG ×160

_ZN

* Residue conservation analysis

Obsolete entry

PDB id:

3knh

Name:

Ribosome/antibiotic

Title:

The structures of viomycin bound to the 70s ribosome. This file contains the 30s subunit for molecule i

Structure:

16s ribosomal RNA. Chain: a. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5.

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Synthetic: yes. Escherichia coli. Organism_taxid: 536056. Strain: dh1. Gene: ecdh1_r0066, glnv glnx, pecwa_r0066. Expressed in: escherichia coli.

Resolution:

3.00Å R-factor: 0.248 R-free: 0.272

Authors:

R.E.Stanley,G.Blaha

Key ref:

R.E.Stanley et al. (2010). The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome. Nat Struct Biol, 17, 289-293. PubMed id: 20154709

Date:

12-Nov-09 Release date: 16-Feb-10

Protein chain

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

Seq: 256 a.a.

Struc: 235 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: 207 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: 151 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

Q5SHQ2  (RS8_THET8) -

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: 99 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: 119 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: 125 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: 120 a.a.

Protein chain

Q5SHQ1  (RS14Z_THET8) -

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: 84 a.a.

Protein chain

Q5SHP7  (RS17_THET8) -

Protein chain

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

Seq: 88 a.a.

Struc: 70 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: 79 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: 25 a.a.

DNA/RNA chains

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-C- ... 1495 bases

A-A-A-A-U-G-C-A-G-U 10 bases

U-G-G-G-G-U-A-U-C-G-C-C-A-A-G-C-G-G-U-A-A-G-G-C-A-C-C-G-G-A-U-U-C-U-G-A-U-U-C- 75 bases

C-G-C-G-G-G-G-U-G-G-A-G-C-A-G-C-C-U-G-G-U-A-G-C-U-C-G-U-C-G-G-G-C-U-C-A-U-A-A- 77 bases

U-G-G-G-G-U-A-U-C-G-C-C-A-A-G-C-G-G-U-A-A-G-G-C-A-C-C-G-G-A-U-U-G-U-G-A-U-U-C- 75 bases

Nat Struct Biol 17:289-293 (2010)

PubMed id: 20154709

The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.

R.E.Stanley, G.Blaha, R.L.Grodzicki, M.D.Strickler, T.A.Steitz.

ABSTRACT

Viomycin and capreomycin belong to the tuberactinomycin family of antibiotics, which are among the most effective antibiotics against multidrug-resistant tuberculosis. Here we present two crystal structures of the 70S ribosome in complex with three tRNAs and bound to either viomycin or capreomycin at 3.3- and 3.5-A resolution, respectively. Both antibiotics bind to the same site on the ribosome, which lies at the interface between helix 44 of the small ribosomal subunit and helix 69 of the large ribosomal subunit. The structures of these complexes suggest that the tuberactinomycins inhibit translocation by stabilizing the tRNA in the A site in the pretranslocation state. In addition, these structures show that the tuberactinomycins bind adjacent to the binding sites for the paromomycin and hygromycin B antibiotics, which may enable the development of new derivatives of tuberactinomycins that are effective against drug-resistant strains.