7QH4 image
Deposition Date 2021-12-10
Release Date 2022-03-16
Last Version Date 2024-07-17
Entry Detail
PDB ID:
7QH4
Keywords:
RIBOSOME
Title:
Structure of the B. subtilis disome - collided 70S ribosome
Biological Source:
Source Organism:
Bacillus subtilis (Taxon ID: 1423)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
5.45 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7QH4 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:A
Chain Length:2928
Number of Molecules:1
Biological Source:Bacillus subtilis
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:B
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Chain IDs:C
Chain Length:49
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P42919 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Chain IDs:D
Chain Length:44
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P42920 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Chain IDs:E
Chain Length:207
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P42921 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:F
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P12877 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L6
Chain IDs:G
Chain Length:218
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P46898 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Chain IDs:H
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P42923 Pfam ID:PF00466
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Chain IDs:I
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:Q06796 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:J
Chain Length:145
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P70974 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:K
Chain Length:122
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P12875 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:L
Chain Length:146
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P19946 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Chain IDs:M
Chain Length:144
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P14577 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:N
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P20277 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:O
Chain Length:131
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P46899 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:P
Chain Length:138
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:O31742 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:Q
Chain Length:119
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P55873 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Chain IDs:R
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P26908 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Chain IDs:S
Chain Length:89
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P42060 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:T
Chain Length:90
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P42924 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:U
Chain Length:103
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P0CI78 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:V
Chain Length:94
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P05657 Pfam ID:PF01016
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:EA (auth: W)
Chain Length:1555
Number of Molecules:1
Biological Source:Bacillus subtilis
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:FA (auth: X)
Chain Length:246
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P21464 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Chain IDs:W (auth: Y)
Chain Length:62
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P37807 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:X (auth: Z)
Chain Length:66
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P12873 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:Y (auth: a)
Chain Length:2928
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P19947 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:Z (auth: b)
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:O34687 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:AA (auth: c)
Chain Length:49
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P56849 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Chain IDs:BA (auth: d)
Chain Length:44
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P05647 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:CA (auth: e)
Chain Length:207
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P55874 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:DA (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P20278 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:GA (auth: g)
Chain Length:218
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P21465 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:HA (auth: h)
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P21466 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:IA (auth: i)
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P21467 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:JA (auth: j)
Chain Length:145
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P21468 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Chain IDs:KA (auth: k)
Chain Length:122
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P21469 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:LA (auth: l)
Chain Length:146
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P12879 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:MA (auth: m)
Chain Length:144
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P21470 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:NA (auth: n)
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P21471 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:OA (auth: o)
Chain Length:131
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P04969 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:PA (auth: p)
Chain Length:138
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P21472 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:QA (auth: q)
Chain Length:119
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P20282 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Chain IDs:RA (auth: r)
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P12878 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:SA (auth: s)
Chain Length:89
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P21473 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:TA (auth: t)
Chain Length:90
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P21474 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:UA (auth: u)
Chain Length:103
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P12874 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:VA (auth: v)
Chain Length:94
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P21475 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:WA (auth: w)
Chain Length:1555
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P21476 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:XA (auth: x)
Chain Length:246
Number of Molecules:1
Biological Source:Bacillus subtilis
UniProt ID:P21477 Pfam ID:PF01649
Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:YA (auth: y), ZA (auth: 1)
Chain Length:77
Number of Molecules:2
Biological Source:Bacillus subtilis
Ligand Molecules
NA
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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Disease

Primary Citation of related structures
7QH4