2UUA

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a Valine-ASL with cmo5U in position 34 bound to an mRNA with a GUC-codon in the A-site and paromomycin.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history. 


Literature

Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines.

Weixlbaumer, A., Murphy 4th., F.V., Dziergowska, A., Malkiewicz, A., Vendeix, F.A., Agris, P.F., Ramakrishnan, V.

(2007) Nat Struct Mol Biol 14: 498-502

  • DOI: https://doi.org/10.1038/nsmb1242
  • Primary Citation of Related Structures:  
    2UU9, 2UUA, 2UUB, 2UUC

  • PubMed Abstract: 

    One of the most prevalent base modifications involved in decoding is uridine 5-oxyacetic acid at the wobble position of tRNA. It has been known for several decades that this modification enables a single tRNA to decode all four codons in a degenerate codon box. We have determined structures of an anticodon stem-loop of tRNA(Val) containing the modified uridine with all four valine codons in the decoding site of the 30S ribosomal subunit. An intramolecular hydrogen bond involving the modification helps to prestructure the anticodon loop. We found unusual base pairs with the three noncomplementary codon bases, including a G.U base pair in standard Watson-Crick geometry, which presumably involves an enol form for the uridine. These structures suggest how a modification in the uridine at the wobble position can expand the decoding capability of a tRNA.

    • Organizational Affiliation: 

    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.


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 
UniProt
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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 
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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 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12135Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13126Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1461Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1589Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1688Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17105Thermus thermophilus HB8Mutation(s): 0 
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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 THX27Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S RRNA1,522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
5'-R(*GP*UP*CP*AP*AP*AP)-3'V [auth X]6Thermus thermophilus HB8
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Entity ID: 23
MoleculeChains LengthOrganismImage
5'-R(*CP*CP*UP*CP*CP*CP*UP*CM0P*AP*CP*6MZP*AP *GP*GP*AP*GP*G)-3'W [auth Y]17Thermus thermophilus HB8
Sequence Annotations
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  • Reference Sequence
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
Download Ideal Coordinates CCD File 
IH [auth N],
ZG [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K
Download Ideal Coordinates CCD File 
AG [auth A]
BG [auth A]
CG [auth A]
DG [auth A]
DH [auth E]
AG [auth A],
BG [auth A],
CG [auth A],
DG [auth A],
DH [auth E],
EG [auth A],
FG [auth A],
GG [auth A],
HG [auth A],
IG [auth A],
JG [auth A],
KG [auth A],
LG [auth A],
MG [auth A],
NG [auth A],
OG [auth A],
PG [auth A],
QG [auth A],
RG [auth A],
SG [auth A],
TG [auth A],
UG [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AH [auth D],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BH [auth E],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CH [auth E],
DA [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EH [auth F],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FH [auth G],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GH [auth H],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HH [auth H],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JH [auth Q],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth A],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth B],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 401.919α = 90
b = 401.919β = 90
c = 174.592γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-12
    Changes: Advisory, Derived calculations
  • Version 2.0: 2019-02-13
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary