4JV5

Crystal structures of pseudouridinilated stop codons with ASLs

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

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: 10.1038/nature12302
  • Structures With Same Primary Citation

  • 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 ...

    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: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10J98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJ, TTHA1693
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11K119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsK, rps11, TTHA1666
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12L125Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsL, TTHA1697
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13M120Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsM, rps13, TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14N60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZ, rpsN, TTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15O88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsO, TTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16P83Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsP, TTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17Q99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQ, TTHA1683
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18R70Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsR, TTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19S78Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsS, TTHA1688
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2B234Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsB, rps2, TTHA0861
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein 20T99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsT, rps20, TTHA1397
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein THXU24Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsU, TTHA1396
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3C206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsC, rps3, TTHA1686
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4D208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsD, rps4, TTHA1665
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5E150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsE, TTHA1675
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6F101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsF, TTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7G155Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsG, rps7, TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8H138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsH, TTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9I127Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsI, rps9, TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1517Thermus thermophilus HB8
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Entity ID: 22
MoleculeChainsLengthOrganism
mRNAX5synthetic construct
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Entity ID: 23
MoleculeChainsLengthOrganism
ASL-tRNAY10synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download CCD File 
A, X, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 401α = 90
b = 401β = 90
c = 176γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2013-08-21
    Changes: Database references