2E5L image
Deposition Date 2006-12-21
Release Date 2007-05-15
Last Version Date 2024-03-13
Entry Detail
PDB ID:
2E5L
Keywords:
RIBOSOME
Title:
A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine- Dalgarno interaction
Biological Source:
Source Organism:
synthetic construct (Taxon ID: 32630)
Thermus thermophilus (Taxon ID: 274)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.30 Å
R-Value Free:
0.30
R-Value Work:
0.25
Space Group:
P 41 21 2
2E5L validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:5'-R(*GP*AP*AP*AP*GP*A)-3'
Chain IDs:B (auth: 1), C (auth: 2)
Chain Length:6
Number of Molecules:2
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A
Chain Length:1520
Number of Molecules:1
Biological Source:Thermus thermophilus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:D (auth: B)
Chain Length:227
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80371 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:E (auth: C)
Chain Length:238
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80372 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:F (auth: D)
Chain Length:208
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:G (auth: E)
Chain Length:161
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:H (auth: F)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SLP8 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:I (auth: G)
Chain Length:155
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P17291 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:J (auth: H)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY9 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:K (auth: I)
Chain Length:128
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80374 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:L (auth: J)
Chain Length:104
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN7 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:M (auth: K)
Chain Length:128
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80376 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:N (auth: L)
Chain Length:131
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN3 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:O (auth: M)
Chain Length:125
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80377 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:P (auth: N)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY6 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:Q (auth: O)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SJ76 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:R (auth: P)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SJH3 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:S (auth: Q)
Chain Length:104
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY7 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:T (auth: R)
Chain Length:87
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:U (auth: S)
Chain Length:92
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP2 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:V (auth: T)
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80380 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:W (auth: V)
Chain Length:26
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SIH3 Pfam ID:PF17070
Ligand Molecules
ZN
Primary Citation
A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction
Structure 15 289 297 (2007)
PMID: 17355865 DOI: 10.1016/j.str.2006.12.008

Abstact

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.

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Disease

Primary Citation of related structures
2E5L