ISDA: 8QPP

Deposition Date 2023-10-02

Release Date 2023-12-27

Last Version Date 2024-10-23

Entry Detail

PDB ID:

8QPP

Keywords:

RIBOSOME

Title:

Bacillus subtilis MutS2-collided disome complex (stalled 70S)

Biological Source:

Source Organism:

Bacillus subtilis (Taxon ID: 1423)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.40 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:A (auth: 0)
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:O34687 Pfam ID:PF01783

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33
Chain IDs:B (auth: 1)
Chain Length:48
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P56849 Pfam ID:PF00471

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34
Chain IDs:C (auth: 2)
Chain Length:44
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P05647 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL35
Chain IDs:D (auth: 3)
Chain Length:66
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P55874 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:E (auth: 4)
Chain Length:37
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P20278 Pfam ID:PF00444

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL31
Chain IDs:F (auth: 6)
Chain Length:64
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:Q03223 Pfam ID:PF01197

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Chain IDs:YA (auth: 9)
Chain Length:149
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P37437 Pfam ID:PF01281, PF03948

Polymer Type:polyribonucleotide
Molecule:16S rRNA (1533-MER)
Chain IDs:AB (auth: A)
Chain Length:1533
Number of Molecules:1
Biological Source:Bacillus subtilis

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:G (auth: B)
Chain Length:205
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P21464 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:H (auth: C)
Chain Length:178
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P21465 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:I (auth: D)
Chain Length:175
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P21466 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:J (auth: E)
Chain Length:142
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P21467 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:K (auth: F)
Chain Length:95
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P21468 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Chain IDs:L (auth: G)
Chain Length:156
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P21469 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:M (auth: H)
Chain Length:132
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P12879 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:N (auth: I)
Chain Length:146
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P21470 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:O (auth: J)
Chain Length:138
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P21471 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:P (auth: K)
Chain Length:119
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P04969 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:Q (auth: L)
Chain Length:138
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P21472 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:R (auth: M)
Chain Length:121
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P20282 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Chain IDs:S (auth: N)
Chain Length:117
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P12878 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:T (auth: O)
Chain Length:101
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P21473 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:U (auth: P)
Chain Length:90
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P21474 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:V (auth: Q)
Chain Length:87
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P12874 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:W (auth: R)
Chain Length:109
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P21475 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:X (auth: S)
Chain Length:92
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P21476 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:Y (auth: T)
Chain Length:88
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P21477 Pfam ID:PF01649

Polymer Type:polyribonucleotide
Molecule:tRNA (77-MER)
Chain IDs:Z (auth: U)
Chain Length:77
Number of Molecules:1
Biological Source:Bacillus subtilis

Polymer Type:polyribonucleotide
Molecule:mRNA (33-MER)
Chain IDs:AA (auth: V)
Chain Length:33
Number of Molecules:1
Biological Source:Bacillus subtilis

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Endonuclease MutS2
Chain IDs:BA (auth: W)
Chain Length:65
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P94545 Pfam ID:PF00488, PF20297, PF01713

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:ZA (auth: X)
Chain Length:58
Number of Molecules:1
Biological Source:Bacillus subtilis

Polymer Type:polyribonucleotide
Molecule:5S rRNA (112-MER)
Chain IDs:CA (auth: Y)
Chain Length:112
Number of Molecules:1
Biological Source:Bacillus subtilis

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Chain IDs:DA (auth: Z)
Chain Length:275
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P42919 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3
Chain IDs:EA (auth: a)
Chain Length:1533
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P42920 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4
Chain IDs:FA (auth: b)
Chain Length:205
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P42921 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5
Chain IDs:GA (auth: c)
Chain Length:178
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P12877 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6
Chain IDs:HA (auth: d)
Chain Length:175
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P46898 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Chain IDs:IA (auth: e)
Chain Length:142
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P70974 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:JA (auth: f)
Chain Length:95
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P12875 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:KA (auth: i)
Chain Length:146
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P19946 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16
Chain IDs:LA (auth: j)
Chain Length:138
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P14577 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL17
Chain IDs:MA (auth: k)
Chain Length:119
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P20277 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:NA (auth: l)
Chain Length:138
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P46899 Pfam ID:PF00861

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:OA (auth: m)
Chain Length:121
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:O31742 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL20
Chain IDs:PA (auth: n)
Chain Length:117
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P55873 Pfam ID:PF00453

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL21
Chain IDs:QA (auth: o)
Chain Length:101
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P26908 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22
Chain IDs:RA (auth: r)
Chain Length:109
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P42060 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Chain IDs:SA (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P42924 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Chain IDs:TA (auth: t)
Chain Length:88
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P0CI78 Pfam ID:PF00467, PF17136

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27
Chain IDs:UA (auth: u)
Chain Length:77
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P05657 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL28
Chain IDs:VA (auth: v)
Chain Length:33
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P37807 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Chain IDs:WA (auth: w)
Chain Length:65
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P12873 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Chain IDs:XA (auth: x)
Chain Length:58
Number of Molecules:1
Biological Source:Bacillus subtilis

UniProt ID:P19947 Pfam ID:PF00327

Ligand Molecules

Primary Citation

B. subtilis MutS2 splits stalled ribosomes into subunits without mRNA cleavage.

Park, E.N, Mackens-Kiani, T, Berhane, R, Esser, H, Erdenebat, C, Burroughs, A.M, Berninghausen, O, Aravind, L, Beckmann, R, Green, R, Buskirk, A.R, Maurina, S.F, O'Sullivan, J.P, Sharma, G, Rodriguez, D.C.P, MacFadden, A, Cendali, F, Henen, M.A, Kieft, J.S, Glasgow, A, Steckelberg, A.Show

Embo J. 43 484 506 (2024)

PMID: 38177497 DOI: 10.1038/s44318-023-00010-3

Abstact

Stalled ribosomes are rescued by pathways that recycle the ribosome and target the nascent polypeptide for degradation. In E. coli, these pathways are triggered by ribosome collisions through the recruitment of SmrB, a nuclease that cleaves the mRNA. In B. subtilis, the related protein MutS2 was recently implicated in ribosome rescue. Here we show that MutS2 is recruited to collisions by its SMR and KOW domains, and we reveal the interaction of these domains with collided ribosomes by cryo-EM. Using a combination of in vivo and in vitro approaches, we show that MutS2 uses its ABC ATPase activity to split ribosomes, targeting the nascent peptide for degradation through the ribosome quality control pathway. However, unlike SmrB, which cleaves mRNA in E. coli, we see no evidence that MutS2 mediates mRNA cleavage or promotes ribosome rescue by tmRNA. These findings clarify the biochemical and cellular roles of MutS2 in ribosome rescue in B. subtilis and raise questions about how these pathways function differently in diverse bacteria.

Legend

Protein

Chemical

Disease

Primary Citation of related structures