PDBsum entry 1nji

Ribosome

PDB id: 1nji

Contents

Protein chains

237 a.a. *

337 a.a. *

246 a.a. *

140 a.a. *

172 a.a. *

119 a.a. *

29 a.a. *

156 a.a. *

142 a.a. *

132 a.a. *

145 a.a. *

194 a.a. *

186 a.a. *

115 a.a. *

143 a.a. *

95 a.a. *

150 a.a. *

81 a.a. *

119 a.a. *

53 a.a. *

65 a.a. *

154 a.a. *

82 a.a. *

142 a.a. *

73 a.a. *

56 a.a. *

46 a.a. *

92 a.a. *

DNA/RNA

Ligands

CLM

Metals

_NA ×85

_CL ×22

_MG ×117

_CD ×5

__K ×2

Waters ×7867

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit.

Authors

J.L.Hansen, P.B.Moore, T.A.Steitz.

Ref.

J Mol Biol, 2003, 330, 1061-1075. [DOI no: 10.1016/S0022-2836(03)00668-5]

PubMed id

12860128

Abstract

Structures of anisomycin, chloramphenicol, sparsomycin, blasticidin S, and virginiamycin M bound to the large ribosomal subunit of Haloarcula marismortui have been determined at 3.0A resolution. Most of these antibiotics bind to sites that overlap those of either peptidyl-tRNA or aminoacyl-tRNA, consistent with their functioning as competitive inhibitors of peptide bond formation. Two hydrophobic crevices, one at the peptidyl transferase center and the other at the entrance to the peptide exit tunnel play roles in binding these antibiotics. Midway between these crevices, nucleotide A2103 of H.marismortui (2062 Escherichia coli) varies in its conformation and thereby contacts antibiotics bound at either crevice. The aromatic ring of anisomycin binds to the active-site hydrophobic crevice, as does the aromatic ring of puromycin, while the aromatic ring of chloramphenicol binds to the exit tunnel hydrophobic crevice. Sparsomycin contacts primarily a P-site bound substrate, but also extends into the active-site hydrophobic crevice. Virginiamycin M occupies portions of both the A and P-site, and induces a conformational change in the ribosome. Blasticidin S base-pairs with the P-loop and thereby mimics C74 and C75 of a P-site bound tRNA.

Figure 3.
Figure 3. Electron density maps. Unbiased F[o] -F[c] difference Fourier maps (gray netting) contoured at 3.0s reveal the location, orientation, and conformation of these antibiotics. (a), (b) Nucleotides of ribosomal RNA (gray sticks) that are either protected or deprotected by the anisomycin (a) or chloramphenicol (b) from chemical modification (green) or that upon mutation confer resistance to the given antibiotic (orange) are provided for context. (c) The placement and conformation of virginiamycin M (blue) in the corresponding doughnut shaped electron density is unambiguous. (d) Blasticidin S (purple) binds at two sites, but density for the second site is weaker and incomplete. (e) Sparsomycin (green) binds only in the presence of a P-site bound substrate (orange). A2637 (2602) (gray stick) is apparent in the difference map because it changes conformation upon substrate binding.

Figure 7.
Figure 7. Sparsomycin binding site. Sparsomycin (green) is sandwiched between the CCA end of P-site bound substrate analogue, CCA-phe-cap-biotin (large spheres) and the base of A2637 (2602) (gray sticks). Hydrogen bonds and ionic interactions are shown as dotted lines. A magnesium ion is purple and water molecules are small red spheres. The sulfur (yellow) containing tail of sparsomycin enters the active-site hydrophobic crevice between A2486 (2451) (gray sticks) and C2487 (2452) (orange sticks, resistance mutation).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 330, 1061-1075) copyright 2003.

Secondary reference #1

Title

The complete atomic structure of the large ribosomal subunit at 2.4 a resolution.

Authors

N.Ban, P.Nissen, J.Hansen, P.B.Moore, T.A.Steitz.

Ref.

Science, 2000, 289, 905-920. [DOI no: 10.1126/science.289.5481.905]

PubMed id

10937989

Figure 1.
Fig. 1. Portions of the experimental 2.4 Å resolution electron density map. (A) A stereo view of a junction between 23S rRNA domains II, III, IV, and V having a complex structure that is clearly interpretable. The electron density is contoured at 2 . The bases are white and the backbones are colored by domain as specified in Fig. 4. (B) The extended region of L3 interacting with its surrounding RNA, where the red RNA density is contoured at 2 and the blue protein density is contoured at 1.5 . (C) Detail in the L2 region showing a bound Mg2+ ion. (D) Detail from L2 showing amino acid side chains. (E) Helices 94 through 97 from domain VI. The red contour level is at 2 , and the yellow contour at 6 shows the positions of the higher electron density phosphate groups.

Figure 2.
Fig. 2. The H. marismortui large ribosomal subunit in the rotated crown view. The L7/L12 stalk is to the right, the L1 stalk is to the left, and the central protuberance (CP) is at the top. In this view, the surface of the subunit that interacts with the small subunit faces the reader. RNA is shown in gray in a pseudo-space-filling rendering. The backbones of the proteins visible are rendered in gold. The Yarus inhibitor bound to the peptidyl transferase site of the subunit is indicated in green (64). The particle is approximately 250 Å across.

The above figures are reproduced from the cited reference with permission from the AAAs

Secondary reference #2

Title

The structural basis of ribosome activity in peptide bond synthesis.

Authors

P.Nissen, J.Hansen, N.Ban, P.B.Moore, T.A.Steitz.

Ref.

Science, 2000, 289, 920-930. [DOI no: 10.1126/science.289.5481.920]

PubMed id

10937990

Figure 1.
Fig. 1. Chemical structures of ribosome peptidyl transferase substrates and analogs. (A) The tetrahedral carbon intermediate produced during peptide bond formation; the tetrahedral carbon is indicated by an arrow. (B) The transition state analog formed by coupling the 3' OH of CCdA to the amino group of the O-methyl tyrosine residue of puromycin via a phosphate group, CCdA-p-Puro (a gift from Michael Yarus) (32). (C) An N-amino-acylated mini-helix constructed to target the A-site. The oligonucleotide sequence 5'-CCGGCGGGCUGGUUCAAACCGGCCCGCCGGA- CC-3' puromycin should form 13 base pairs. The construct is based on a mini-helix known to be a suitable substrate for amino-acylation by Tyr-tRNA synthetase. The 3' OH of its terminal C is coupled to the 5' OH of the N6-dimethyl A moiety of puromycin by a phosphodiester bond.

Figure 7.
Fig. 7. Conserved nucleotides in the peptidyl transferase region with bound CCdA-p-Puro. A space-filling representation of the active site region with the Yarus inhibitor viewed down the active site cleft. All atoms belonging to 23S rRNA nucleotides that are >95% conserved in all three kingdoms (44) are colored red and all other nucleotides are white; the inhibitor is colored blue.

The above figures are reproduced from the cited reference with permission from the AAAs