8QBT image
Deposition Date 2023-08-25
Release Date 2024-03-20
Last Version Date 2025-03-12
Entry Detail
PDB ID:
8QBT
Keywords:
RIBOSOME
Title:
E. coli ApdP-stalled ribosomal complex
Biological Source:
Source Organism:
Sinorhizobium medicae (Taxon ID: 110321)
Escherichia coli BW25113 (Taxon ID: 679895)
Host Organism:
Escherichia coli BW25113
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8QBT validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
Gene (Uniprot):rpsS
Chain IDs:RA (auth: 1)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7U3 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:SA (auth: 2)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7U7 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS21
Gene (Uniprot):rpsU
Chain IDs:TA (auth: 3)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P68679 Pfam ID:PF01165
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:UA (auth: 4)
Chain Length:10
Number of Molecules:1
Biological Source:Sinorhizobium medicae
Polymer Type:polyribonucleotide
Molecule:Pro-tRNA
Chain IDs:VA (auth: 5), WA (auth: 6)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Molecule:Ala-tRNA
Chain IDs:XA (auth: 7)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:A
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:B
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Gene (Uniprot):rplB
Chain IDs:C
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Chain IDs:D
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P60438 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4
Gene (Uniprot):rplD
Chain IDs:E
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P60723 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5
Gene (Uniprot):rplE
Chain IDs:F
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P62399 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:G
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG55 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL9
Gene (Uniprot):rplI
Chain IDs:H
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rplM
Chain IDs:I (auth: J)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AA10 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14
Gene (Uniprot):rplN
Chain IDs:J (auth: K)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0ADY3 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:K (auth: L)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P02413 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Chain IDs:L (auth: M)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0ADY7 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL17
Gene (Uniprot):rplQ
Chain IDs:M (auth: N)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG44 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):rplR
Chain IDs:N (auth: O)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0C018 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL19
Gene (Uniprot):rplS
Chain IDs:O (auth: P)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7K6 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:P (auth: Q)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7L3 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL21
Gene (Uniprot):rplU
Chain IDs:Q (auth: R)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG48 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22
Gene (Uniprot):rplV
Chain IDs:R (auth: S)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P61175 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:S (auth: T)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0ADZ0 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Gene (Uniprot):rplX
Chain IDs:T (auth: U)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P60624 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:U (auth: V)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P68919 Pfam ID:PF01386
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27
Gene (Uniprot):rpmA
Chain IDs:V (auth: W)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7L8 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL28
Gene (Uniprot):rpmB
Chain IDs:W (auth: X)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7M2 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Gene (Uniprot):rpmC
Chain IDs:X (auth: Y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7M6 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:Y (auth: Z)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG51 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL32
Gene (Uniprot):rpmF
Chain IDs:Z (auth: a)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7N4 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33
Gene (Uniprot):rpmG
Chain IDs:AA (auth: b)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7N9 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34
Gene (Uniprot):rpmH
Chain IDs:BA (auth: c)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7P5 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL35
Gene (Uniprot):rpmI
Chain IDs:CA (auth: d)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7Q1 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL36A
Gene (Uniprot):rpmJ
Chain IDs:YA (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7Q6 Pfam ID:PF00444
Polymer Type:polypeptide(L)
Molecule:ApdP nascent chain
Chain IDs:ZA (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Sinorhizobium medicae
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:DA (auth: i)
Chain Length:1540
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:EA (auth: j)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7V0 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
Gene (Uniprot):rpsE
Chain IDs:FA (auth: m)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6, fully modified isoform
Gene (Uniprot):rpsF
Chain IDs:GA (auth: n)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P02358 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:HA (auth: o)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P02359 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Gene (Uniprot):rpsH
Chain IDs:IA (auth: p)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7W7 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Gene (Uniprot):rpsI
Chain IDs:JA (auth: q)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7X3 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:KA (auth: s)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7R9 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:LA (auth: t)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7S3 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
Gene (Uniprot):rpsM
Chain IDs:MA (auth: u)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7S9 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
Gene (Uniprot):rpsN
Chain IDs:NA (auth: v)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG59 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Gene (Uniprot):rpsO
Chain IDs:OA (auth: w)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0ADZ4 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Gene (Uniprot):rpsQ
Chain IDs:PA (auth: y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG63 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS18
Gene (Uniprot):rpsR
Chain IDs:QA (auth: z)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7T7 Pfam ID:PF01084
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MA A A modified residue
PSU A 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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Disease

Primary Citation of related structures
8QBT
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