8QCQ image
Deposition Date 2023-08-28
Release Date 2024-03-20
Last Version Date 2025-03-12
Entry Detail
PDB ID:
8QCQ
Keywords:
RIBOSOME
Title:
B. subtilis ApdA-stalled ribosomal complex
Biological Source:
Source Organism:
Amycolatopsis japonica (Taxon ID: 208439)
Bacillus subtilis subsp. subtilis str. 168 (Taxon ID: 224308)
Host Organism:
Bacillus subtilis subsp. subtilis str. 168
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8QCQ validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:A (auth: 0)
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:O34687 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33 1
Gene (Uniprot):rpmGA
Chain IDs:B (auth: 1)
Chain Length:49
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P56849 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:C (auth: 2)
Chain Length:44
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P05647 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:D (auth: 3)
Chain Length:66
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P55874 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:E (auth: 4)
Chain Length:37
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P20278 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL31-A
Gene (Uniprot):rpmE
Chain IDs:F (auth: 6)
Chain Length:65
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:Q03223 Pfam ID:PF01197
Polymer Type:polypeptide(L)
Molecule:ApdA nascent chain
Chain IDs:XA (auth: 7)
Chain Length:9
Number of Molecules:1
Biological Source:Amycolatopsis japonica
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:MA (auth: 8)
Chain Length:6
Number of Molecules:1
Biological Source:Amycolatopsis japonica
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:G (auth: A)
Chain Length:1554
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:H (auth: B)
Chain Length:119
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:I (auth: C)
Chain Length:277
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42919 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:J (auth: D)
Chain Length:209
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42920 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:K (auth: E)
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42921 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:L (auth: F)
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12877 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6
Gene (Uniprot):rplF
Chain IDs:M (auth: G)
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P46898 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:N (auth: J)
Chain Length:145
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P70974 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:O (auth: K)
Chain Length:131
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12875 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:P (auth: L)
Chain Length:138
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P19946 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:Q (auth: M)
Chain Length:121
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P14577 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:R (auth: N)
Chain Length:61
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P20277 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:S (auth: O)
Chain Length:89
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P46899 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:T (auth: P)
Chain Length:115
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:O31742 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL20
Gene (Uniprot):rplT
Chain IDs:U (auth: Q)
Chain Length:119
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P55873 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:V (auth: R)
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P26908 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:W (auth: S)
Chain Length:92
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42060 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Gene (Uniprot):rplW
Chain IDs:X (auth: T)
Chain Length:88
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42924 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:Y (auth: U)
Chain Length:103
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P0CI78 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27
Gene (Uniprot):rpmA
Chain IDs:Z (auth: W)
Chain Length:94
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P05657 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:AA (auth: X)
Chain Length:62
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P37807 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:BA (auth: Y)
Chain Length:66
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12873 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):rpmD
Chain IDs:CA (auth: Z)
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P19947 Pfam ID:PF00327
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:DA (auth: a)
Chain Length:1554
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):rpsC
Chain IDs:NA (auth: c)
Chain Length:277
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21465 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:EA (auth: e)
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21467 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:WA (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21468 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Gene (Uniprot):rpsG
Chain IDs:OA (auth: g)
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21469 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:UA (auth: h)
Chain Length:132
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12879 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:PA (auth: i)
Chain Length:130
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21470 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:QA (auth: j)
Chain Length:145
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21471 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:FA (auth: k)
Chain Length:131
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P04969 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:GA (auth: l)
Chain Length:138
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21472 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:RA (auth: m)
Chain Length:121
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P20282 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN1
Chain IDs:SA (auth: n)
Chain Length:61
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12878 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:HA (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21473 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:IA (auth: q)
Chain Length:119
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12874 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:VA (auth: r)
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21475 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:TA (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21476 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:JA (auth: t)
Chain Length:88
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21477 Pfam ID:PF01649
Polymer Type:polyribonucleotide
Molecule:Pro-tRNA
Chain IDs:KA (auth: y), LA (auth: w)
Chain Length:94
Number of Molecules:2
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MA G A modified residue
OMG G G modified residue
PSU G U modified residue
Ligand Molecules
K
MG
PRO
ZN
Primary Citation
RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity.
Nat Commun 15 2432 2432 (2024)
PMID: 38503735 DOI: 10.1038/s41467-024-46761-3

Abstact

Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein localization machinery components. Here we determine cryo-EM structures of ribosomes stalled on RAPP arrest motifs in both Bacillus subtilis and Escherichia coli. Together with molecular dynamics simulations, our structures reveal that the RAPP motifs allow full accommodation of the A-site tRNA, but prevent the subsequent peptide bond from forming. Our data support a model where the RAP in the P-site interacts and stabilizes a single hydrogen atom on the Pro-tRNA in the A-site, thereby preventing an optimal geometry for the nucleophilic attack required for peptide bond formation to occur. This mechanism to short circuit the ribosomal peptidyltransferase activity is likely to operate for the majority of other RAPP-like arrest peptides found across diverse bacterial phylogenies.

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Protein

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Disease

Primary Citation of related structures
8QCQ
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