5ME0 image
Deposition Date 2016-11-14
Release Date 2017-01-11
Last Version Date 2024-04-24
Entry Detail
PDB ID:
5ME0
Keywords:
RIBOSOME
Title:
Structure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled by GE81112
Biological Source:
Source Organism:
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (Taxon ID: 300852)
Escherichia coli K-12 (Taxon ID: 83333)
Geobacillus stearothermophilus (Taxon ID: 1422)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
13.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5ME0 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A
Chain Length:1534
Number of Molecules:1
Biological Source:Escherichia coli K-12
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7V0 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:C
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:D
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:E
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:F
Chain Length:131
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P02358 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:G
Chain Length:156
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P02359 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:H
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7W7 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7X3 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:J
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7R5 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:K
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7R9 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:L
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7S3 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:M
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7S9 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:N
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG59 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:O
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0ADZ4 Pfam ID:PF00312
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:P
Chain Length:102
Number of Molecules:1
Biological Source:Escherichia coli K-12
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:Q
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG63 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:R
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7T7 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:S
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7U3 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:T
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7U7 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:U
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P68679 Pfam ID:PF01165
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Translation initiation factor IF-1
Gene (Uniprot):infA
Chain IDs:V
Chain Length:72
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHR1 Pfam ID:PF01176
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Translation initiation factor IF-2
Gene (Uniprot):infB
Chain IDs:W
Chain Length:890
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A705 Pfam ID:PF04760, PF08364, PF00009, PF22042, PF11987, PF03144 EC:3.6.5.3
Polymer Type:polyribonucleotide
Molecule:fMet-tRNA
Chain IDs:Z (auth: X)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli K-12
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Translation initiation factor IF-3
Gene (Uniprot):infC
Chain IDs:X (auth: Y)
Chain Length:171
Number of Molecules:1
Biological Source:Geobacillus stearothermophilus
UniProt ID:P03000 Pfam ID:PF05198, PF00707
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Translation initiation factor IF-3
Gene (Uniprot):infC
Chain IDs:Y (auth: Z)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A707 Pfam ID:PF05198, PF00707
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG A G modified residue
4OC A C modified residue
4SU Z U modified residue
5MC A C modified residue
5MU Z U modified residue
D2T L ASP modified residue
G7M A G modified residue
H2U Z U modified residue
MA6 A A modified residue
PSU A U modified residue
UR3 A U modified residue
Ligand Molecules
FME
Primary Citation
Structure of a 30S pre-initiation complex stalled by GE81112 reveals structural parallels in bacterial and eukaryotic protein synthesis initiation pathways.
Nucleic Acids Res. 45 2179 2187 (2017)
PMID: 27986852 DOI: 10.1093/nar/gkw1251

Abstact

In bacteria, the start site and the reading frame of the messenger RNA are selected by the small ribosomal subunit (30S) when the start codon, typically an AUG, is decoded in the P-site by the initiator tRNA in a process guided and controlled by three initiation factors. This process can be efficiently inhibited by GE81112, a natural tetrapeptide antibiotic that is highly specific toward bacteria. Here GE81112 was used to stabilize the 30S pre-initiation complex and obtain its structure by cryo-electron microscopy. The results obtained reveal the occurrence of changes in both the ribosome conformation and initiator tRNA position that may play a critical role in controlling translational fidelity. Furthermore, the structure highlights similarities with the early steps of initiation in eukaryotes suggesting that shared structural features guide initiation in all kingdoms of life.

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Disease

Primary Citation of related structures
5ME0