7QH4 image
Entry Detail
PDB ID:
7QH4
EMDB ID:
Keywords:
Title:
Structure of the B. subtilis disome - collided 70S ribosome
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2021-12-10
Release Date:
2022-03-16
Method Details:
Experimental Method:
Resolution:
5.45 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:23S rRNA
Chain IDs:A
Chain Length:2928
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:B
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:C
Chain Length:49
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:D
Chain Length:44
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:E
Chain Length:207
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:F
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:Ribosomal protein L6
Chain IDs:G
Chain Length:218
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L10
Chain IDs:H
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L11
Chain IDs:I
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:J
Chain Length:145
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:K
Chain Length:122
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:L
Chain Length:146
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:M
Chain Length:144
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:N
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:O
Chain Length:131
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:P
Chain Length:138
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:Q
Chain Length:119
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:R
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:S
Chain Length:89
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:T
Chain Length:90
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:U
Chain Length:103
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:V
Chain Length:94
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polyribonucleotide
Description:16S rRNA
Chain IDs:EA (auth: W)
Chain Length:1555
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:FA (auth: X)
Chain Length:246
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:W (auth: Y)
Chain Length:62
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:X (auth: Z)
Chain Length:66
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:Y (auth: a)
Chain Length:2928
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:Z (auth: b)
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:AA (auth: c)
Chain Length:49
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:BA (auth: d)
Chain Length:44
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:CA (auth: e)
Chain Length:207
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:DA (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:GA (auth: g)
Chain Length:218
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:HA (auth: h)
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:IA (auth: i)
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6
Chain IDs:JA (auth: j)
Chain Length:145
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:KA (auth: k)
Chain Length:122
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:LA (auth: l)
Chain Length:146
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:MA (auth: m)
Chain Length:144
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:NA (auth: n)
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:OA (auth: o)
Chain Length:131
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:PA (auth: p)
Chain Length:138
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:QA (auth: q)
Chain Length:119
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14 type Z
Chain IDs:RA (auth: r)
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:SA (auth: s)
Chain Length:89
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:TA (auth: t)
Chain Length:90
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:UA (auth: u)
Chain Length:103
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:VA (auth: v)
Chain Length:94
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:WA (auth: w)
Chain Length:1555
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:XA (auth: x)
Chain Length:246
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polyribonucleotide
Description:tRNA
Chain IDs:YA (auth: y), ZA (auth: 1)
Chain Length:77
Number of Molecules:2
Biological Source:Bacillus subtilis
Ligand Molecules
Primary Citation
Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria.
Nature 603 503 508 (2022)
PMID: 35264790 DOI: 10.1038/s41586-022-04416-7

Abstact

Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation1,2. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the middle of a transcript from actively translating ribosomes3-6. Here, using a genetic screen in Escherichia coli, we discovered a new rescue factor that has endonuclease activity. SmrB cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA (which acts on truncated mRNAs3) to rescue upstream ribosomes. SmrB is recruited to ribosomes and is activated by collisions. Cryo-electron microscopy structures of collided disomes from E. coli and Bacillus subtilis show distinct and conserved arrangements of individual ribosomes and the composite SmrB-binding site. These findings reveal the underlying mechanisms by which ribosome collisions trigger ribosome rescue in bacteria.

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Primary Citation of related structures