1N34

Structure of the Thermus thermophilus 30S ribosomal subunit in the presence of codon and crystallographically disordered near-cognate transfer rna anticodon stem-loop mismatched at the first codon position


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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.

(2002) Cell 111: 721-732

  • DOI: https://doi.org/10.1016/s0092-8674(02)01086-3
  • Primary Citation of Related Structures:  
    1N32, 1N33, 1N34, 1N36

  • PubMed 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.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, CB2 2QH, Cambridge, United Kingdom.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2C [auth B]256Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3D [auth C]239Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4E [auth D]208Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5F [auth E]161Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6G [auth F]101Thermus thermophilusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7H [auth G]155Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8I [auth H]138Thermus thermophilusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9J [auth I]128Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10K [auth J]104Thermus thermophilusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11L [auth K]129Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12M [auth L]135Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13N [auth M]126Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14O [auth N]60Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15P [auth O]88Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16Q [auth P]88Thermus thermophilusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17R [auth Q]104Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18S [auth R]88Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19T [auth S]92Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20U [auth T]106Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THX26Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S RIBOSOMAL RNA1,522Thermus thermophilus
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Entity ID: 2
MoleculeChains LengthOrganismImage
A-SITE MESSENGER RNA FRAGMENTB [auth Z]6Thermus thermophilus
Sequence Annotations
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Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
RNA PDBBind:  1N34 Kd: 2.20e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 401.844α = 90
b = 401.844β = 90
c = 173.854γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-29
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description