6DTI

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with an unmodifed anticodon stem loop (ASL) of Escherichia coli transfer RNA Arginine 2 (TRNAARG2) bound to an mRNA with an CGU-codon in the A-site and paromomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.54 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

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This is version 1.4 of the entry. See complete history


Literature

A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine.

Vangaveti, S.Cantara, W.A.Spears, J.L.DeMirci, H.Murphy IV, F.V.Ranganathan, S.V.Sarachan, K.L.Agris, P.F.

(2020) J Mol Biol 432: 913-929

  • DOI: https://doi.org/10.1016/j.jmb.2019.12.016
  • Primary Citation of Related Structures:  
    6DTI, 6MKN, 6MPF, 6MPI

  • PubMed Abstract: 

    Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli tRNA Arg isoacceptors. The anticodon stem and loop (ASL) domains of tRNA Arg1 and tRNA Arg2 both contain inosine and 2-methyladenosine modifications at positions 34 (I 34 ) and 37 (m 2 A 37 ). tRNA Arg1 is also modified from cytidine to 2-thiocytidine at position 32 (s 2 C 32 ). The s 2 C 32 modification is known to negate wobble codon recognition of the rare CGA codon by an unknown mechanism, while still allowing decoding of CGU and CGC. Substitution of s 2 C 32 for C 32 in the Saccharomyces cerevisiae tRNA Ile IAU anticodon stem and loop domain (ASL) negates wobble decoding of its synonymous A-ending codon, suggesting that this function of s 2 C at position 32 is a generalizable property. X-ray crystal structures of variously modified ASL Arg1 ICG and ASL Arg2 ICG constructs bound to cognate and wobble codons on the ribosome revealed the disruption of a C 32- A 38 cross-loop interaction but failed to fully explain the means by which s 2 C 32 restricts I 34 wobbling. Computational studies revealed that the adoption of a spatially broad inosine-adenosine base pair at the wobble position of the codon cannot be maintained simultaneously with the canonical ASL U-turn motif. C 32- A 38 cross-loop interactions are required for stability of the anticodon/codon interaction in the ribosomal A-site.


  • Organizational Affiliation

    The RNA Institute, University at Albany-SUNY, 1400 Washington Ave., Albany, NY, 12222, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2256Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3239Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4209Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5162Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6101Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7156Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8138Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11129Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12132Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type Z61Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1589Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1688Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17105Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1888Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1993Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20106Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxU [auth V]27Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16s rRNA1,507Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
tRNA ASL Escherichia coli Arg2V [auth X]17Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
mRNA A-site fragment6Escherichia coli
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Small Molecules
Ligands 2 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
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth A]
AD [auth A]
BA [auth A]
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth E],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth J],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth J],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth K],
OA [auth A],
OB [auth A],
OC [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.54 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 404.54α = 90
b = 404.54β = 90
c = 176.62γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2RO1GM23037-25
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM110588-01
National Science Foundation (NSF, United States)United StatesMCB1101859
National Science Foundation (NSF, United States)United StatesCHE1407042

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.2: 2020-01-29
    Changes: Database references
  • Version 1.3: 2020-03-11
    Changes: Database references, Source and taxonomy
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary