4JI4

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.69 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The central role of protein S12 in organizing the structure of the decoding site of the ribosome.

Demirci, H., Wang, L., Murphy, F.V., Murphy, E.L., Carr, J.F., Blanchard, S.C., Jogl, G., Dahlberg, A.E., Gregory, S.T.

(2013) RNA 19: 1791-1801

  • DOI: 10.1261/rna.040030.113
  • Primary Citation of Related Structures:  
    4JI3, 4JI4, 4JI5, 4JI6, 4JI7, 4JI8, 4JI0, 4JI1, 4JI2

  • PubMed Abstract: 

    • The ribosome decodes mRNA by monitoring the geometry of codon-anticodon base-pairing using a set of universally conserved 16S rRNA nucleotides within the conformationally dynamic decoding site. By applying single-molecule FRET and X-ray crystallography, ...

    The ribosome decodes mRNA by monitoring the geometry of codon-anticodon base-pairing using a set of universally conserved 16S rRNA nucleotides within the conformationally dynamic decoding site. By applying single-molecule FRET and X-ray crystallography, we have determined that conditional-lethal, streptomycin-dependence mutations in ribosomal protein S12 interfere with tRNA selection by allowing conformational distortions of the decoding site that impair GTPase activation of EF-Tu during the tRNA selection process. Distortions in the decoding site are reversed by streptomycin or by a second-site suppressor mutation in 16S rRNA. These observations encourage a refinement of the current model for decoding, wherein ribosomal protein S12 and the decoding site collaborate to optimize codon recognition and substrate discrimination during the early stages of the tRNA selection process.

    Organizational Affiliation: 

    Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 90187, Sweden.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S2 B256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsB, rps2, TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S3 C239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsC, rps3, TTHA1686
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S4 D209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsD, rps4, TTHA1665
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S5 E162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsE, TTHA1675
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
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RIBOSOMAL PROTEIN S6 F101Thermus 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
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RIBOSOMAL PROTEIN S7 G156Thermus 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
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RIBOSOMAL PROTEIN S8 H138Thermus 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
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RIBOSOMAL PROTEIN S9 I128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsI, rps9, TTHA1464
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Entity ID: 10
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RIBOSOMAL PROTEIN S10 J105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJ, TTHA1693
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Entity ID: 11
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RIBOSOMAL PROTEIN S11 K129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsK, rps11, TTHA1666
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Entity ID: 12
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RIBOSOMAL PROTEIN S12 L135Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsL, TTHA1697
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Entity ID: 13
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RIBOSOMAL PROTEIN S13 M126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsM, rps13, TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S14 N61Thermus 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 LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S15 O89Thermus 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
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RIBOSOMAL PROTEIN S16 P88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsP, TTHA1035
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Entity ID: 17
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RIBOSOMAL PROTEIN S17 Q105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQ, TTHA1683
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S18 R88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsR, TTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S19 S93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsS, TTHA1688
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 20
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RIBOSOMAL PROTEIN S20 T106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsT, rps20, TTHA1397
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN THX U27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsU, TTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1522Thermus thermophilus HB8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
A, B, C, D, E, F, H, I, J, P, Q
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD		LL-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.69 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 402.081α = 90
b = 402.081β = 90
c = 174.609γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2013-12-04
    Changes: Database references