2E5L

A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine- Dalgarno interaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction

Kaminishi, T.Wilson, D.N.Takemoto, C.Harms, J.M.Kawazoe, M.Schluenzen, F.Hanawa-Suetsugu, K.Shirouzu, M.Fucini, P.Yokoyama, S.

(2007) Structure 15: 289-297

  • DOI: 10.1016/j.str.2006.12.008
  • Primary Citation of Related Structures:  
    2E5L

  • PubMed Abstract: 
  • In the initiation phase of bacterial translation, the 30S ribosomal subunit captures mRNA in preparation for binding with initiator tRNA. The purine-rich Shine-Dalgarno (SD) sequence, in the 5' untranslated region of the mRNA, anchors the 30S subunit ...

    In the initiation phase of bacterial translation, the 30S ribosomal subunit captures mRNA in preparation for binding with initiator tRNA. The purine-rich Shine-Dalgarno (SD) sequence, in the 5' untranslated region of the mRNA, anchors the 30S subunit near the start codon, via base pairing with an anti-SD (aSD) sequence at the 3' terminus of 16S rRNA. Here, we present the 3.3 A crystal structure of the Thermus thermophilus 30S subunit bound with an mRNA mimic. The duplex formed by the SD and aSD sequences is snugly docked in a "chamber" between the head and platform domains, demonstrating how the 30S subunit captures and stabilizes the otherwise labile SD helix. This location of the SD helix is suitable for the placement of the start codon AUG in the immediate vicinity of the mRNA channel, in agreement with reported crosslinks between the second position of the start codon and G1530 of 16S rRNA.


    Organizational Affiliation

    RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D208Thermus thermophilusMutation(s): 0 
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E161Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F101Thermus thermophilusMutation(s): 0 
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7G155Thermus thermophilusMutation(s): 0 
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8H138Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9I128Thermus thermophilusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10J104Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11K128Thermus thermophilusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12L131Thermus thermophilusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13M125Thermus thermophilusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14N60Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15O88Thermus thermophilusMutation(s): 0 
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16P88Thermus thermophilusMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17Q104Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19S92Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T105Thermus thermophilusMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxV26Thermus thermophilusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18R87Thermus thermophilusMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B227Thermus thermophilusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C238Thermus thermophilusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA1520Thermus thermophilus
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(*GP*AP*AP*AP*GP*A)-3'1, 26synthetic construct
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download CCD File 
    D, N
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.30 Å
    • R-Value Free: 0.301 
    • R-Value Work: 0.259 
    • Space Group: P 41 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 411.79α = 90
    b = 411.79β = 90
    c = 173.16γ = 90
    Software Package:
    Software NamePurpose
    XSCALEdata scaling
    MOLREPphasing
    CNSrefinement
    PDB_EXTRACTdata extraction
    XDSdata scaling
    XDSdata reduction

    Structure Validation

    View Full Validation Report



    Entry History 

    Revision History 

    • Version 1.0: 2007-05-15
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2019-12-11
      Changes: Advisory, Derived calculations, Source and taxonomy