PDBsum entry: 1n33

Ribosome

PDB-id: 1n33

Asymmetric unit

Main view

Contents

Description

Header details

Header records

References

PROCHECK

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. *

118 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

Ligands

PAR

Metal ions

_MG ×106

_ZN ×2

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit*, 23mer
(*as deduced by PQS)

PDB id:

1n33

Name:

Ribosome

Title:

Structure of the thermus thermophilus 30s ribosomal subunit bound to codon and near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position at the a site with paromomycin

Structure:

16s ribosomal RNA. Chain: a. Anticodon stem-loop of ser transfer RNA. Chain: y. A-site messenger RNA fragment. Chain: z. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3.

Source:

Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274

Biological unit:

23mer (from PQS)

UniProt:

Chain B: P80371 (RS2_THET8)

Seq:	256 a.a.
Struc:	234 a.a.

Chain C: P80372 (RS3_THET8)

Seq:	239 a.a.
Struc:	206 a.a.

Chain D: P80373 (RS4_THET8)

Seq:	209 a.a.
Struc:	208 a.a.

Chain E: Q5SHQ5 (RS5_THET8)

Seq:	162 a.a.
Struc:	150 a.a.

Chain F: Q5SLP8 (RS6_THET8)

Seq:	101 a.a.
Struc:	101 a.a.

Chain G: P17291 (RS7_THET8)

Seq:	156 a.a.
Struc:	155 a.a.

Chain H: Q5SHQ2 (RS8_THET8)

Seq:	138 a.a.
Struc:	138 a.a.

Chain I: P80374 (RS9_THET8)

Seq:	128 a.a.
Struc:	127 a.a.*

Chain J: Q5SHN7 (RS10_THET8)

Seq:	105 a.a.
Struc:	98 a.a.

Chain K: P80376 (RS11_THET8)

Seq:	129 a.a.
Struc:	119 a.a.

Chain L: Q5SHN3 (RS12_THET8)

Seq:	132 a.a.
Struc:	124 a.a.

Chain M: P80377 (RS13_THET8)

Seq:	126 a.a.
Struc:	118 a.a.

Chain N: Q5SHQ1 (RS14Z_THET8)

Seq:	61 a.a.
Struc:	60 a.a.

Chain O: Q5SJ76 (RS15_THET8)

Seq:	89 a.a.
Struc:	88 a.a.

Chain P: Q5SJH3 (RS16_THET8)

Seq:	88 a.a.
Struc:	83 a.a.

Chain Q: Q5SHP7 (RS17_THET8)

Seq:	105 a.a.
Struc:	104 a.a.*

Chain R: Q5SLQ0 (RS18_THET8)

Seq:	88 a.a.
Struc:	73 a.a.*

Chain S: Q5SHP2 (RS19_THET8)

Seq:	93 a.a.
Struc:	80 a.a.

Chain T: P80380 (RS20_THET8)

Seq:	106 a.a.
Struc:	99 a.a.

Chain V: Q5SIH3 (RSHX_THET8)

Seq:

27 a.a.

Struc:

24 a.a.

Key:	PfamA domain	PfamB domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Resolution:

3.35Å

R-factor:

0.225

R-free:

0.284

Authors:

J.M.Ogle,F.V.Murphy Iv,M.J.Tarry,V.Ramakrishnan

Key ref:

J.M.Ogle et al. (2002). Selection of tRNA by the ribosome requires a transition from an open to a closed form.. Cell, 111, 721-732. [PubMed id: 12464183] [DOI: 10.1016/S0092-8674(02)01086-3]

Date:

25-Oct-02

Release date:

29-Nov-02

Related entries:

1j5e
native structure of the 30s particle
1fjg
structure of the 30s particle in complex with the
antibiotics streptomycin, spectinomycin and paromomycin
1ibl
structure of the 30s particle in complex with messenger RNA
fragment and cognate transfer RNA anticodon stem-loop bound
to the a site and with the antibiotic paromomycin
1ibk
... plus others (see Header records)

Quick_links

Procheck

Key reference

DOI no: 10.1016/S0092-8674(02)01086-3

Cell 111:721-732 (2002)

PubMed id: 12464183

Selection of tRNA by the ribosome requires a transition from an open to a closed form.

J.M.Ogle, F.V.Murphy, M.J.Tarry, V.Ramakrishnan.

ABSTRACT

A structural and mechanistic explanation for the selection of tRNAs by the ribosome has been elusive. Here, we report crystal structures of the 30S ribosomal subunit with codon and near-cognate tRNA anticodon stem loops bound at the decoding center and compare affinities of equivalent complexes in solution. In ribosomal interactions with near-cognate tRNA, deviation from Watson-Crick geometry results in uncompensated desolvation of hydrogen-bonding partners at the codon-anticodon minor groove. As a result, the transition to a closed form of the 30S induced by cognate tRNA is unfavorable for near-cognate tRNA unless paromomycin induces part of the rearrangement. We conclude that stabilization of a closed 30S conformation is required for tRNA selection, and thereby structurally rationalize much previous data on translational fidelity.

Selected figure(s)

Figure 3.
Figure 3. Discrimination at the First Two Codon Positions(A) Refined 2mF[o]-DF[c] electron density (contoured at 1.2 σ) from the ASL^Leu2/paromomycin structure for the anticodon-codon G:U mismatch at the first position and A1493.(B) Superposition of the ASL^Leu2/paromomycin structure (dark red), on the corresponding cognate interaction (gray, A:U anticodon-codon base pair; Ogle et al., 2001), in which dashed lines connect hydrogen bond donors and acceptors and the line of larger, transparent red spheres highlights the uncompensated loss of a hydrogen bond caused by separation of A1493 and the codon. The last two images show van der Waals surfaces for the near-cognate and cognate structures, respectively.(C) Electron density from the ASL^Ser/paromomycin structure around the second codon position, showing A1492 and G530. The appropriate position of a guanine base to pair with the refined position of the codon U is shown in light gray; the expected position of a uridine base forming a typical base pair with the refined position of anticodon G is shown in dark gray.(D) G530 at the second codon position, showing mF[o]-DF[c] difference electron density (contoured at 3 σ) obtained when the base is omitted from refinement. Superpositions are based upon the 5′-domain of the 16S RNA. In the native structure, the density clearly represents the syn conformation (cyan, Wimberly et al., 2000, G530 in the anti conformation from the ASL^Ser/paromomycin structure is superimposed, blue). In the ASL^Ser/paromomycin structure (blue), density is weaker, arising from partial disorder due to the G:U mismatch at the second codon position (the native syn structure is superimposed, in cyan). In the ASL^Leu2/paromomycin structure (red), the density unambiguously represents the anti conformation.

Figure 5.
Figure 5. Details of Movements at the S4-S5 Interface and the Region around S12E. coli numbering is used for RNA residues and in parentheses for protein residues.(A) Proteins S4 and S5, on the back of the subunit body/shoulder region, move apart due to 30S closure. Based on rigid phosphorus atoms in the 16S RNA identified using ESCET, the ASL^Leu2/paromomycin structure (red) is superimposed on the native structure (gray), in which known mutations causing the error-prone ram phenotype are marked green.(B) The same structure comparison as in (A), showing the formation of contacts between protein S12, and helices 44 and 27 of 16S RNA due the closing rearrangement in the body. Mutations that cause hyperaccurate translation or modulate streptomycin sensitivity are marked green. Streptomycin (from the superimposed 30S complex, pdb-code 1FJG, Carter et al., 2000) is shown for reference.Please see Supplemental Data for animation of these changes (available at http://www.cell.com/cgi/content/full/111/5/721/DC1).

The above figures are reprinted by permission from Cell Press: Cell (2002, 111, 721-732) copyright 2002.

Figures were selected by the author.