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: https://doi.org/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 near the start codon, via base pairing with an anti-SD (aSD) sequence at the 3' terminus of 16S rRNA ...

    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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2D [auth B]227Thermus thermophilusMutation(s): 0 
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Entity ID: 4
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30S ribosomal protein S3E [auth C]238Thermus thermophilusMutation(s): 0 
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Entity ID: 5
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30S ribosomal protein S4F [auth D]208Thermus thermophilusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5G [auth E]161Thermus thermophilusMutation(s): 0 
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Entity ID: 7
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30S ribosomal protein S6H [auth F]101Thermus thermophilusMutation(s): 0 
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Entity ID: 8
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30S ribosomal protein S7I [auth G]155Thermus thermophilusMutation(s): 0 
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30S ribosomal protein S8J [auth H]138Thermus thermophilusMutation(s): 0 
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30S ribosomal protein S9K [auth I]128Thermus thermophilusMutation(s): 0 
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Entity ID: 11
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30S ribosomal protein S10L [auth J]104Thermus thermophilusMutation(s): 0 
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30S ribosomal protein S11M [auth K]128Thermus thermophilusMutation(s): 0 
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30S ribosomal protein S12N [auth L]131Thermus thermophilusMutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13O [auth M]125Thermus thermophilusMutation(s): 0 
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30S ribosomal protein S14P [auth N]60Thermus thermophilusMutation(s): 0 
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30S ribosomal protein S15Q [auth O]88Thermus thermophilusMutation(s): 0 
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Entity ID: 17
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30S ribosomal protein S16R [auth P]88Thermus thermophilusMutation(s): 0 
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30S ribosomal protein S17S [auth Q]104Thermus thermophilusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18T [auth R]87Thermus thermophilusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19U [auth S]92Thermus thermophilusMutation(s): 0 
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Entity ID: 21
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30S ribosomal protein S20V [auth T]105Thermus thermophilusMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxW [auth V]26Thermus thermophilusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA1,520Thermus thermophilus
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*GP*AP*AP*AP*GP*A)-3'B [auth 1],
C [auth 2]		6synthetic construct
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
X [auth D],
Y [auth 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

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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: 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