ISDA

Deposition Date 2023-11-29

Release Date 2024-07-24

Last Version Date 2025-03-12

Entry Detail

PDB ID:

8R8M

Keywords:

RIBOSOME

Title:

70S Escherichia coli ribosome with Paenilamicin B2 bound with hybrid A/P- and hybrid P/E-tRNA.

Biological Source:

Source Organism:

synthetic construct (Taxon ID: 32630)
Escherichia coli BW25113 (Taxon ID: 679895)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.40 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download 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:EA (auth: 4)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7M9 Pfam ID:PF01197

Polymer Type:polypeptide(L)
Molecule:Paenilamicin B2
Chain IDs:DB (auth: 5)
Chain Length:8
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:GA (auth: A)
Chain Length:2903
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:OA (auth: B)
Chain Length:241
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:HA (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:PA (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:QA (auth: E)
Chain Length:167
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:RA (auth: F)
Chain Length:179
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:NA (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:SA (auth: H)
Chain Length:149
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:IA (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:JA (auth: J)
Chain Length:103
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:ZA (auth: K)
Chain Length:129
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:AB (auth: L)
Chain Length:124
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:KA (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:LA (auth: N)
Chain Length:117
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:TA (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:UA (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:VA (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:WA (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:MA (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:XA (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:YA (auth: U)
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:DA (auth: X)
Chain Length:10
Number of Molecules:1
Biological Source:Escherichia coli BW25113

Polymer Type:polyribonucleotide
Molecule:Isoleucine-tRNA
Chain IDs:CB (auth: Y)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli BW25113

Polymer Type:polyribonucleotide
Molecule:Leucine-tRNA
Chain IDs:BB (auth: Z)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli BW25113

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:FA (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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Gene (Uniprot):rplB
Chain IDs:F (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:G (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:H (auth: e)
Chain Length:167
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:I (auth: f)
Chain Length:179
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:J (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:K (auth: h)
Chain Length:149
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:L (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:M (auth: j)
Chain Length:103
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:N (auth: k)
Chain Length:129
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:O (auth: l)
Chain Length:124
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:P (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:Q (auth: n)
Chain Length:117
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:R (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:S (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:T (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:U (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:V (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:W (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:X (auth: u)
Chain Length:71
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:Y (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:Z (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:AA (auth: x)
Chain Length:10
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:BA (auth: y)
Chain Length:59
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:CA (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
2MG	GA	G	modified residue
4D4	O	ARG	modified residue
4OC	GA	C	modified residue
5MC	GA	C	modified residue
D2T	AB	ASP	modified residue
G7M	GA	G	modified residue
MEQ	G	GLN	modified residue
MIA	BB	A	modified residue
MKX	CB	A	modified residue
PSU	GA	U	modified residue
UR3	GA	U	modified residue

Ligand Molecules

Peptide-like Molecules

PRD_002555

Primary Citation

Paenilamicins from the honey bee pathogen Paenibacillus larvae are context-specific translocation inhibitors of protein synthesis.

Koller, T.O, Berger, M.J, Morici, M, Paternoga, H, Bulatov, T, Di Stasi, A, Dang, T, Mainz, A, Raulf, K, Crowe-McAuliffe, C, Scocchi, M, Mardirossian, M, Beckert, B, Vazquez-Laslop, N, Mankin, A, Sussmuth, R.D, Wilson, D.N.Show

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