ISDA

Entry Detail

PDB ID:

1N33

Keywords:

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

Biological Source:

Source Organism:

Thermus thermophilus

PDB Version:

Deposition Date:

2002-10-25

Release Date:

2002-11-29

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.35 Å

R-Value Free:

0.28

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 41 21 2

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Description:16S RIBOSOMAL RNA
Chain IDs:A
Chain Length:1522
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S2
Chain IDs:D (auth: B)
Chain Length:256
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80371 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S3
Chain IDs:E (auth: C)
Chain Length:239
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S4
Chain IDs:F (auth: D)
Chain Length:208
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S5
Chain IDs:G (auth: E)
Chain Length:161
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S6
Chain IDs:H (auth: F)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLP8 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S7
Chain IDs:I (auth: G)
Chain Length:155
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P17291 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S8
Chain IDs:J (auth: H)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P0DOY9 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S9
Chain IDs:K (auth: I)
Chain Length:128
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80374 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S10
Chain IDs:L (auth: J)
Chain Length:104
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN7 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S11
Chain IDs:M (auth: K)
Chain Length:129
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80376 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S12
Chain IDs:N (auth: L)
Chain Length:135
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S13
Chain IDs:O (auth: M)
Chain Length:126
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80377 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S14
Chain IDs:P (auth: N)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P0DOY6 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S15
Chain IDs:Q (auth: O)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SJ76 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S16
Chain IDs:R (auth: P)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SJH3 Pfam ID:PF00886

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S17
Chain IDs:S (auth: Q)
Chain Length:104
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P0DOY7 Pfam ID:PF00366

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S18
Chain IDs:T (auth: R)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S19
Chain IDs:U (auth: S)
Chain Length:92
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP2 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S20
Chain IDs:V (auth: T)
Chain Length:106
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80380 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN THX
Chain IDs:W (auth: V)
Chain Length:26
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Description:ANTICODON STEM-LOOP OF SER TRANSFER RNA
Chain IDs:B (auth: Y)
Chain Length:17
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Description:A-SITE MESSENGER RNA FRAGMENT
Chain IDs:C (auth: Z)
Chain Length:6
Number of Molecules:1
Biological Source:Thermus thermophilus

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
PSU	B	U	PSEUDOURIDINE-5'-MONOPHOSPHATE

Ligand Molecules

PAR

Primary Citation

Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form

Ogle, J.M, Murphy IV, F.V, Tarry, M.J, Ramakrishnan, V, Ogle, J.M, Brodersen, D.E, Clemons Jr, W.M, Tarry, M.J, Carter, A.P, Ramakrishnan, V, Wimberly, B.T, Brodersen, D.E, Clemons Jr, W.M, Morgan-Warren, R, Carter, A.P, Vonrhein, C, Hartsch, T, Ramakrishnan, V, Carter, A.P, Clemons Jr, W.M, Brodersen, D.E, Wimberly, B.T, Morgan-Warren, R, Ramakrishnan, V.Show

Cell(Cambridge,Mass.) 111 721 732 (2002)

PMID: 12464183 DOI: 10.1016/S0092-8674(02)01086-3

Abstact

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.

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Protein

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Disease

Primary Citation of related structures