2UXD

Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA CGGG in the context of the Thermus thermophilus 30S subunit.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 

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This is version 2.3 of the entry. See complete history


Literature

Structures of Trnas with an Expanded Anticodon Loop in the Decoding Center of the 30S Ribosomal Subunit.

Dunham, C.M.Selmer, M.Phelps, S.S.Kelley, A.C.Suzuki, T.Joseph, S.Ramakrishnan, V.

(2007) RNA 13: 817

  • DOI: https://doi.org/10.1261/rna.367307
  • Primary Citation of Related Structures:  
    2UXB, 2UXC, 2UXD

  • PubMed Abstract: 

    During translation, some +1 frameshift mRNA sites are decoded by frameshift suppressor tRNAs that contain an extra base in their anticodon loops. Similarly engineered tRNAs have been used to insert nonnatural amino acids into proteins. Here, we report crystal structures of two anticodon stem-loops (ASLs) from tRNAs known to facilitate +1 frameshifting bound to the 30S ribosomal subunit with their cognate mRNAs. ASL(CCCG) and ASL(ACCC) (5'-3' nomenclature) form unpredicted anticodon-codon interactions where the anticodon base 34 at the wobble position contacts either the fourth codon base or the third and fourth codon bases. In addition, we report the structure of ASL(ACGA) bound to the 30S ribosomal subunit with its cognate mRNA. The tRNA containing this ASL was previously shown to be unable to facilitate +1 frameshifting in competition with normal tRNAs (Hohsaka et al. 2001), and interestingly, it displays a normal anticodon-codon interaction. These structures show that the expanded anticodon loop of +1 frameshift promoting tRNAs are flexible enough to adopt conformations that allow three bases of the anticodon to span four bases of the mRNA. Therefore it appears that normal triplet pairing is not an absolute constraint of the decoding center.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S2256Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S3239Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S4209Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S5162Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S6101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S7156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S8138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S9128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S10105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S11129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S12135Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S13126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S1461Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S1589Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S1688Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S17105Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S1888Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S1993Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S20106Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN THXU [auth V]27Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S RIBOSOMAL RNA1,523Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
ANTICODON STEM-LOOP OF TRANSFER RNA WITH ANTICODON CCCGV [auth X]4synthetic construct
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Entity ID: 23
MoleculeChains LengthOrganismImage
A-SITE MESSENGER RNA FRAGMENT CGGGW [auth Y]18synthetic construct
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download Ideal Coordinates CCD File 
X [auth A]PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
ZN
Query on ZN

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YC [auth G],
ZC [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
QC [auth G]
RC [auth G]
SC [auth G]
TC [auth G]
UC [auth G]
QC [auth G],
RC [auth G],
SC [auth G],
TC [auth G],
UC [auth G],
VC [auth G],
WC [auth G],
XC [auth G]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth G]
AB [auth G]
AC [auth G]
BA [auth G]
BB [auth G]
AA [auth G],
AB [auth G],
AC [auth G],
BA [auth G],
BB [auth G],
BC [auth G],
CA [auth G],
CB [auth G],
CC [auth G],
DA [auth G],
DB [auth G],
DC [auth G],
EA [auth G],
EB [auth G],
EC [auth G],
FA [auth G],
FB [auth G],
FC [auth G],
GA [auth G],
GB [auth G],
GC [auth G],
HA [auth G],
HB [auth G],
HC [auth G],
IA [auth G],
IB [auth G],
IC [auth G],
JA [auth G],
JB [auth G],
JC [auth G],
KA [auth G],
KB [auth G],
KC [auth G],
LA [auth G],
LB [auth G],
LC [auth G],
MA [auth G],
MB [auth G],
MC [auth G],
NA [auth G],
NB [auth G],
NC [auth G],
OA [auth G],
OB [auth G],
OC [auth G],
PA [auth G],
PB [auth G],
PC [auth G],
QA [auth G],
QB [auth G],
RA [auth G],
RB [auth G],
SA [auth G],
SB [auth G],
TA [auth G],
TB [auth G],
UA [auth G],
UB [auth G],
VA [auth G],
VB [auth G],
WA [auth G],
WB [auth G],
XA [auth G],
XB [auth G],
Y [auth G],
YA [auth G],
YB [auth G],
Z [auth G],
ZA [auth G],
ZB [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 401.903α = 90
b = 401.903β = 90
c = 174.435γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2012-09-19
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2012-10-10
    Changes: Derived calculations
  • Version 2.0: 2018-04-18
    Changes: Advisory, Atomic model, Data collection, Source and taxonomy
  • Version 2.1: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 2.2: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 2.3: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations, Other