9FBV image
Deposition Date 2024-05-14
Release Date 2024-06-26
Last Version Date 2026-04-01
Entry Detail
PDB ID:
9FBV
Keywords:
RIBOSOME
Title:
70S Escherichia coli ribosome with P-site initiatior tRNA.
Biological Source:
Source Organism(s):
Escherichia coli BW25113 (Taxon ID: 679895)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9FBV validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmE
Chain IDs:CA (auth: 4)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7M9 Pfam ID:PF01197
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:AB (auth: A)
Chain Length:2903
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:FA (auth: B)
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 prote
Gene (Uniprot):rpsC
Chain IDs:TA (auth: C)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsD
Chain IDs:GA (auth: D)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsE
Chain IDs:HA (auth: E)
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, ful
Gene (Uniprot):rpsF
Chain IDs:IA (auth: F)
Chain Length:179
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:UA (auth: G)
Chain Length:177
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 prote
Gene (Uniprot):rpsH
Chain IDs:JA (auth: H)
Chain Length:130
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 prote
Gene (Uniprot):rpsI
Chain IDs:VA (auth: I)
Chain Length:130
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:Small ribosomal subunit prote
Gene (Uniprot):rpsJ
Chain IDs:WA (auth: J)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7R5 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsK
Chain IDs:KA (auth: K)
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:Small ribosomal subunit prote
Gene (Uniprot):rpsL
Chain IDs:LA (auth: L)
Chain Length:136
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 prote
Gene (Uniprot):rpsM
Chain IDs:XA (auth: M)
Chain Length:118
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 prote
Gene (Uniprot):rpsN
Chain IDs:YA (auth: N)
Chain Length:101
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 prote
Gene (Uniprot):rpsO
Chain IDs:MA (auth: O)
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:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:NA (auth: P)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7T3 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsQ
Chain IDs:OA (auth: Q)
Chain Length:84
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 prote
Gene (Uniprot):rpsR
Chain IDs:PA (auth: R)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7T7 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsS
Chain IDs:ZA (auth: S)
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:QA (auth: T)
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 prote
Gene (Uniprot):rpsU
Chain IDs:RA (auth: U)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P68679 Pfam ID:PF01165
Polymer Type:polyribonucleotide
Molecule:messenger RNA
Chain IDs:SA (auth: X)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Molecule:fMet-tRNA
Chain IDs:BB (auth: Z)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:DA (auth: a)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:E (auth: b)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplB
Chain IDs:F (auth: c)
Chain Length:233
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:Large ribosomal subunit prote
Gene (Uniprot):rplC
Chain IDs:G (auth: d)
Chain Length:206
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 prote
Gene (Uniprot):rplD
Chain IDs:H (auth: e)
Chain Length:167
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 prote
Gene (Uniprot):rplE
Chain IDs:I (auth: 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 prote
Gene (Uniprot):rplF
Chain IDs:J (auth: 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 prote
Gene (Uniprot):rplI
Chain IDs:K (auth: h)
Chain Length:130
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 prote
Gene (Uniprot):rplM
Chain IDs:L (auth: i)
Chain Length:130
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 prote
Gene (Uniprot):rplN
Chain IDs:EA (auth: j)
Chain Length:103
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:M (auth: k)
Chain Length:129
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:Large ribosomal subunit prote
Gene (Uniprot):rplP
Chain IDs:N (auth: l)
Chain Length:136
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 prote
Gene (Uniprot):rplQ
Chain IDs:O (auth: m)
Chain Length:118
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 prote
Gene (Uniprot):rplR
Chain IDs:P (auth: n)
Chain Length:101
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 prote
Gene (Uniprot):rplS
Chain IDs:Q (auth: o)
Chain Length:89
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 prote
Gene (Uniprot):rplT
Chain IDs:R (auth: p)
Chain Length:82
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 prote
Gene (Uniprot):rplU
Chain IDs:S (auth: q)
Chain Length:84
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 prote
Gene (Uniprot):rplV
Chain IDs:T (auth: r)
Chain Length:75
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 prote
Gene (Uniprot):rplW
Chain IDs:U (auth: s)
Chain Length:92
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 prote
Gene (Uniprot):rplX
Chain IDs:V (auth: t)
Chain Length:87
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:W (auth: u)
Chain Length:71
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 prote
Gene (Uniprot):rpmA
Chain IDs:X (auth: v)
Chain Length:85
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 prote
Gene (Uniprot):rpmB
Chain IDs:Y (auth: w)
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 prote
Gene (Uniprot):rpmC
Chain IDs:Z (auth: x)
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 prote
Gene (Uniprot):rpmD
Chain IDs:AA (auth: y)
Chain Length:59
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 prote
Gene (Uniprot):rpmF
Chain IDs:BA (auth: z)
Chain Length:57
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 AB G modified residue
4D4 N ARG modified residue
4OC AB C modified residue
5MC AB C modified residue
D2T LA ASP modified residue
G7M AB G modified residue
MEQ G GLN modified residue
PSU AB U modified residue
UR3 AB U modified residue
Ligand Molecules
K
MG
ZN
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
8R6C
8R8M
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