7P3K image
Entry Detail
PDB ID:
7P3K
EMDB ID:
Keywords:
Title:
Cryo-EM structure of 70S ribosome stalled with TnaC peptide (control)
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2021-07-08
Release Date:
2021-10-27
Method Details:
Experimental Method:
Resolution:
2.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:VA (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:WA (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:XA (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:YA (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L31
Chain IDs:ZA (auth: 4)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polyribonucleotide
Description:16S rRNA
Chain IDs:A
Chain Length:2753
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:B
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:C
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:D
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:E
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6
Chain IDs:F
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:G
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:H
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:I
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:J
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:K
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:L
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:M
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14
Chain IDs:N
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:O
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:P
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:Q
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:R
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:S
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:T
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S21
Chain IDs:U
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polyribonucleotide
Description:tRNA
Chain IDs:BB (auth: V)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:AB (auth: X)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Description:23S rRNA
Chain IDs:V (auth: a)
Chain Length:2753
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:W (auth: b)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:X (auth: c)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:Y (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:Z (auth: e)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:AA (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:BA (auth: g)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:CA (auth: h)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:DA (auth: i)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:EA (auth: j)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:FA (auth: k)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:GA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:HA (auth: m)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:IA (auth: n)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:JA (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:KA (auth: p)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:LA (auth: q)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:MA (auth: r)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:NA (auth: s)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:OA (auth: t)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:PA (auth: u)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:QA (auth: v)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:RA (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:SA (auth: x)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:TA (auth: y)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:UA (auth: z)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MEQ Y GLN modified residue
Primary Citation
Structural basis of l-tryptophan-dependent inhibition of release factor 2 by the TnaC arrest peptide.
Nucleic Acids Res. 49 9539 9547 (2021)
PMID: 34403461 DOI: 10.1093/nar/gkab665

Abstact

In Escherichia coli, elevated levels of free l-tryptophan (l-Trp) promote translational arrest of the TnaC peptide by inhibiting its termination. However, the mechanism by which translation-termination by the UGA-specific decoding release factor 2 (RF2) is inhibited at the UGA stop codon of stalled TnaC-ribosome-nascent chain complexes has so far been ambiguous. This study presents cryo-EM structures for ribosomes stalled by TnaC in the absence and presence of RF2 at average resolutions of 2.9 and 3.5 Å, respectively. Stalled TnaC assumes a distinct conformation composed of two small α-helices that act together with residues in the peptide exit tunnel (PET) to coordinate a single L-Trp molecule. In addition, while the peptidyl-transferase center (PTC) is locked in a conformation that allows RF2 to adopt its canonical position in the ribosome, it prevents the conserved and catalytically essential GGQ motif of RF2 from adopting its active conformation in the PTC. This explains how translation of the TnaC peptide effectively allows the ribosome to function as a L-Trp-specific small-molecule sensor that regulates the tnaCAB operon.

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Primary Citation of related structures