8R6C image
Deposition Date 2023-11-22
Release Date 2024-07-24
Last Version Date 2025-03-12
Entry Detail
PDB ID:
8R6C
Keywords:
RIBOSOME
Title:
70S Escherichia coli ribosome with Paenilamicin B2 bound with A- and P-site tRNA.
Biological Source:
Source Organism:
synthetic construct (Taxon ID: 32630)
Escherichia coli BW25113 (Taxon ID: 679895)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8R6C validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33
Gene (Uniprot):rpmG
Chain IDs:A (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7N9 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34
Gene (Uniprot):rpmH
Chain IDs:B (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7P5 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL35
Gene (Uniprot):rpmI
Chain IDs:C (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7Q1 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL36A
Gene (Uniprot):rpmJ
Chain IDs:D (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7Q6 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL31A
Gene (Uniprot):rpmE
Chain IDs:E (auth: 4)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7M9 Pfam ID:PF01197
Polymer Type:polyribonucleotide
Molecule:N-Formylmethionine tRNA
Chain IDs:F (auth: 5)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Molecule:Paenilamicin B2
Chain IDs:EB (auth: 6)
Chain Length:8
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:G (auth: A)
Chain Length:1534
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:H (auth: B)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7V0 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):rpsC
Chain IDs:I (auth: C)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
Gene (Uniprot):rpsD
Chain IDs:J (auth: D)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
Gene (Uniprot):rpsE
Chain IDs:K (auth: E)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6, fully modified isoform
Gene (Uniprot):rpsF
Chain IDs:L (auth: F)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P02358 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:M (auth: G)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P02359 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Gene (Uniprot):rpsH
Chain IDs:N (auth: H)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7W7 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Gene (Uniprot):rpsI
Chain IDs:O (auth: I)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7X3 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Gene (Uniprot):rpsJ
Chain IDs:P (auth: J)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7R5 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS11
Gene (Uniprot):rpsK
Chain IDs:Q (auth: K)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7R9 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Gene (Uniprot):rpsL
Chain IDs:R (auth: L)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7S3 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
Gene (Uniprot):rpsM
Chain IDs:S (auth: M)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7S9 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
Gene (Uniprot):rpsN
Chain IDs:T (auth: N)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG59 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Gene (Uniprot):rpsO
Chain IDs:U (auth: O)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0ADZ4 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:V (auth: P)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7T3 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Gene (Uniprot):rpsQ
Chain IDs:W (auth: Q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG63 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS18
Gene (Uniprot):rpsR
Chain IDs:X (auth: R)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7T7 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
Gene (Uniprot):rpsS
Chain IDs:Y (auth: S)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7U3 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:Z (auth: T)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7U7 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS21
Gene (Uniprot):rpsU
Chain IDs:AA (auth: U)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P68679 Pfam ID:PF01165
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:BA (auth: X)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Molecule:Isoeucine-tRNA
Chain IDs:CA (auth: Y)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Molecule:Leucine-tRNA
Chain IDs:DA (auth: Z)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:EA (auth: a)
Chain Length:1534
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:FA (auth: b)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Gene (Uniprot):rplB
Chain IDs:GA (auth: c)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3
Gene (Uniprot):rplC
Chain IDs:HA (auth: d)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P60438 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4
Gene (Uniprot):rplD
Chain IDs:IA (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P60723 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5
Gene (Uniprot):rplE
Chain IDs:JA (auth: f)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P62399 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6
Gene (Uniprot):rplF
Chain IDs:KA (auth: g)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG55 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL9
Gene (Uniprot):rplI
Chain IDs:LA (auth: h)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rplM
Chain IDs:MA (auth: i)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AA10 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14
Gene (Uniprot):rplN
Chain IDs:NA (auth: j)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0ADY3 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:OA (auth: k)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P02413 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16
Gene (Uniprot):rplP
Chain IDs:PA (auth: l)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0ADY7 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL17
Gene (Uniprot):rplQ
Chain IDs:QA (auth: m)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG44 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):rplR
Chain IDs:RA (auth: n)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0C018 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL19
Gene (Uniprot):rplS
Chain IDs:SA (auth: o)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7K6 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL20
Gene (Uniprot):rplT
Chain IDs:TA (auth: p)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7L3 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL21
Gene (Uniprot):rplU
Chain IDs:UA (auth: q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG48 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22
Gene (Uniprot):rplV
Chain IDs:VA (auth: r)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P61175 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Gene (Uniprot):rplW
Chain IDs:WA (auth: s)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0ADZ0 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Gene (Uniprot):rplX
Chain IDs:XA (auth: t)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P60624 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:YA (auth: u)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P68919 Pfam ID:PF01386
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27
Gene (Uniprot):rpmA
Chain IDs:ZA (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7L8 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL28
Gene (Uniprot):rpmB
Chain IDs:AB (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7M2 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Gene (Uniprot):rpmC
Chain IDs:BB (auth: x)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7M6 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):rpmD
Chain IDs:CB (auth: y)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG51 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL32
Gene (Uniprot):rpmF
Chain IDs:DB (auth: z)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7N4 Pfam ID:PF01783
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG G G modified residue
4D4 PA ARG modified residue
4OC G C modified residue
5MC G C modified residue
D2T R ASP modified residue
G7M G G modified residue
MEQ HA GLN modified residue
MIA DA A modified residue
MKX CA A modified residue
PSU G U modified residue
UR3 G U modified residue
Ligand Molecules
K
MG
ZN
Peptide-like Molecules
PRD_002555
Primary Citation
Paenilamicins from the honey bee pathogen Paenibacillus larvae are context-specific translocation inhibitors of protein synthesis.
Biorxiv ? ? ? (2024)
PMID: 38826346 DOI: 10.1101/2024.05.21.595107

Abstact

The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen Paenibacillus larvae that display activity against Gram-positive pathogens, such as Staphylococcus aureus. While paenilamicins have been shown to inhibit protein synthesis, their mechanism of action has remained unclear. Here, we have determined structures of the paenilamicin PamB2 stalled ribosomes, revealing a unique binding site on the small 30S subunit located between the A- and P-site tRNAs. In addition to providing a precise description of interactions of PamB2 with the ribosome, the structures also rationalize the resistance mechanisms utilized by P. larvae. We could further demonstrate that PamB2 interferes with the translocation of mRNA and tRNAs through the ribosome during translation elongation, and that this inhibitory activity is influenced by the presence of modifications at position 37 of the A-site tRNA. Collectively, our study defines the paenilamicins as a new class of context-specific translocation inhibitors.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
8R8M
9FBV