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
  • Structures With Same Primary Citation

  • 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: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
B
227Thermus thermophilusMutation(s): 0 
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
C
238Thermus thermophilusMutation(s): 0 
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
D
208Thermus thermophilusMutation(s): 0 
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
E
161Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
F
101Thermus thermophilusMutation(s): 0 
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
G
155Thermus thermophilusMutation(s): 0 
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
H
138Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
I
128Thermus thermophilusMutation(s): 0 
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
J
104Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
K
128Thermus thermophilusMutation(s): 0 
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
L
131Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
M
125Thermus thermophilusMutation(s): 0 
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
O
88Thermus thermophilusMutation(s): 0 
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
P
88Thermus thermophilusMutation(s): 0 
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
Q
104Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY7

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
R
87Thermus thermophilusMutation(s): 0 
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
S
92Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
T
105Thermus thermophilusMutation(s): 0 
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
V
26Thermus thermophilusMutation(s): 0 
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
N
60Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY6

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1520Thermus thermophilus
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
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