4V9I

Crystal structure of thermus thermophilus 70S in complex with tRNAs and mRNA containing a pseudouridine in a stop codon

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Unusual base pairing during the decoding of a stop codon by the ribosome.

Fernandez, I.S., Ng, C.L., Kelley, A.C., Wu, G., Yu, Y.T., Ramakrishnan, V.

(2013) Nature 500: 107-110

  • DOI: https://doi.org/10.1038/nature12302
  • Primary Citation of Related Structures:  
    4JV5, 4JYA, 4K0K, 4V9I

  • PubMed Abstract: 

    During normal translation, the binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in the termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (Ψ) allows efficient recognition and read-through of these stop codons by a transfer RNA (tRNA), although it requires the formation of two normally forbidden purine-purine base pairs. Here we determined the crystal structure at 3.1 Å resolution of the 30S ribosomal subunit in complex with the anticodon stem loop of tRNA(Ser) bound to the ΨAG stop codon in the A site. The ΨA base pair at the first position is accompanied by the formation of purine-purine base pairs at the second and third positions of the codon, which show an unusual Watson-Crick/Hoogsteen geometry. The structure shows a previously unsuspected ability of the ribosomal decoding centre to accommodate non-canonical base pairs.

    • Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S2B [auth AB],
HB [auth CB]		234Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S3C [auth AC],
IB [auth CC]		206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S4D [auth AD],
JB [auth CD]		208Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S5E [auth AE],
KB [auth CE]		150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S6F [auth AF],
LB [auth CF]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S7G [auth AG],
MB [auth CG]		155Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S8H [auth AH],
NB [auth CH]		138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S9I [auth AI],
OB [auth CI]		127Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S10J [auth AJ],
PB [auth CJ]		98Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S11K [auth AK],
QB [auth CK]		119Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S12L [auth AL],
RB [auth CL]		124Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S13M [auth AM],
SB [auth CM]		124Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S14N [auth AN],
TB [auth CN]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S15O [auth AO],
UB [auth CO]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S16P [auth AP],
VB [auth CP]		83Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S17Q [auth AQ],
WB [auth CQ]		99Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S18R [auth AR],
XB [auth CR]		70Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S19S [auth AS],
YB [auth CS]		78Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein S20T [auth AT],
ZB [auth CT]		99Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal protein THXAC [auth CU],
U [auth AU]		24Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1BA [auth BC]206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2CA [auth BD],
IC [auth DD]		271Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3DA [auth BE],
JC [auth DE]		204Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4EA [auth BF],
KC [auth DF]		207Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5FA [auth BG],
LC [auth DG]		181Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6GA [auth BH],
MC [auth DH]		159Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9HA [auth BI],
NC [auth DI]		145Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10IA [auth BJ],
OC [auth DJ]		130Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13JA [auth BN],
PC [auth DN]		138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14KA [auth BO],
QC [auth DO]		122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15LA [auth BP],
RC [auth DP]		146Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16MA [auth BQ],
SC [auth DQ]		141Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17NA [auth BR],
TC [auth DR]		117Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18OA [auth BS],
UC [auth DS]		98Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19PA [auth BT],
VC [auth DT]		137Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20QA [auth BU],
WC [auth DU]		117Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21RA [auth BV],
XC [auth DV]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22SA [auth BW],
YC [auth DW]		113Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23TA [auth BX],
ZC [auth DX]		92Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24AD [auth DY],
UA [auth BY]		100Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25BD [auth DZ],
VA [auth BZ]		176Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27CD [auth D0],
WA [auth B0]		84Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28DD [auth D1],
XA [auth B1]		93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29ED [auth D2],
YA [auth B2]		71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30FD [auth D3],
ZA [auth B3]		59Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31AB [auth B4],
GD [auth D4]		30Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32BB [auth B5],
HD [auth D5]		59Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33CB [auth B6],
ID [auth D6]		44Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34DB [auth B7],
JD [auth D7]		48Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35EB [auth B8],
KD [auth D8]		63Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36FB [auth B9],
LD [auth D9]		36Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal protein L1HC [auth DC]196Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth AA],
GB [auth CA]		1,504Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
P-SITE tRNABC [auth CV],
V [auth AV]		77Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
E-SITE tRNACC [auth CW],
W [auth AW]		76Escherichia coli
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Entity ID: 24
MoleculeChains LengthOrganismImage
A-SITE tRNADC [auth CY],
X [auth AY]		75Escherichia coli
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Entity ID: 25
MoleculeChains LengthOrganismImage
mRNAY [auth AX]7synthetic construct
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Entity ID: 26
MoleculeChains LengthOrganismImage
23S ribosomal RNAFC [auth DA],
Z [auth BA]		2,915Thermus thermophilus HB8
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Entity ID: 27
MoleculeChains LengthOrganismImage
5S ribosomal RNAAA [auth BB],
GC [auth DB]		119Thermus thermophilus HB8
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Entity ID: 59
MoleculeChains LengthOrganismImage
mRNAEC [auth CX]4synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.92α = 90
b = 449.9β = 90
c = 624.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOLREPphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary