ISDA: 7NSP

Deposition Date 2021-03-08

Release Date 2021-08-11

Last Version Date 2024-10-16

Entry Detail

PDB ID:

7NSP

Keywords:

RIBOSOME

Title:

Structure of ErmDL-Erythromycin-stalled 70S E. coli ribosomal complex with A and P-tRNA

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.50 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:Z (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:AA (auth: 1)
Chain Length:50
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:BA (auth: 2)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7P5 Pfam ID:PF00468

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:CA (auth: 3)
Chain Length:64
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:DA (auth: 4)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7Q6 Pfam ID:PF00444

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Chain IDs:EA (auth: 5)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:FA (auth: 6)
Chain Length:6
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:ermDL
Chain IDs:GA (auth: 7)
Chain Length:7
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:P-tRNA (leu)
Chain IDs:HA (auth: 8)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:A
Chain Length:1540
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:B
Chain Length:224
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60422 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:D
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60438 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E
Chain Length:157
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60723 Pfam ID:PF00573

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:F
Chain Length:99
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:G
Chain Length:151
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:H
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:I (auth: J)
Chain Length:98
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AA10 Pfam ID:PF00572

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:J (auth: K)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli

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:123
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02413 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:L (auth: M)
Chain Length:114
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADY7 Pfam ID:PF00252

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:M (auth: N)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:N (auth: O)
Chain Length:88
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:O (auth: P)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:P (auth: Q)
Chain Length:80
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:Q (auth: R)
Chain Length:66
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG48 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:R (auth: S)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P61175 Pfam ID:PF00237

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:S (auth: T)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:T (auth: U)
Chain Length:102
Number of Molecules:1
Biological Source:Escherichia coli

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

UniProt ID:P68919 Pfam ID:PF01386

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:V (auth: W)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Chain IDs:W (auth: X)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:X (auth: Y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7M6 Pfam ID:PF00831

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:Y (auth: Z)
Chain Length:58
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:IA (auth: a)
Chain Length:1540
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:JA (auth: b)
Chain Length:224
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:KA (auth: c)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:LA (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:MA (auth: e)
Chain Length:157
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:NA (auth: f)
Chain Length:99
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:W8T6F0 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:OA (auth: g)
Chain Length:151
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02359 Pfam ID:PF00177

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:PA (auth: h)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:QA (auth: i)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:RA (auth: j)
Chain Length:98
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:SA (auth: k)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:A0A5I5F5V9 Pfam ID:PF00411

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:TA (auth: l)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:UA (auth: m)
Chain Length:114
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:VA (auth: n)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:WA (auth: o)
Chain Length:88
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:XA (auth: p)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:C3SYP2 Pfam ID:PF00886

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:YA (auth: q)
Chain Length:80
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:ZA (auth: r)
Chain Length:66
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:AB (auth: s)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:BB (auth: t)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Chain IDs:CB (auth: u)
Chain Length:102
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:A-tRNA (Arg)
Chain IDs:DB (auth: v)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli

Ligand Molecules

ERY

Primary Citation

Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics.

Beckert, B, Leroy, E.C, Sothiselvam, S, Bock, L.V, Svetlov, M.S, Graf, M, Arenz, S, Abdelshahid, M, Seip, B, Grubmuller, H, Mankin, A.S, Innis, C.A, Vazquez-Laslop, N, Wilson, D.N.Show

Nat Commun 12 4466 4466 (2021)

PMID: 34294725 DOI: 10.1038/s41467-021-24674-9

Abstact

Macrolides and ketolides comprise a family of clinically important antibiotics that inhibit protein synthesis by binding within the exit tunnel of the bacterial ribosome. While these antibiotics are known to interrupt translation at specific sequence motifs, with ketolides predominantly stalling at Arg/Lys-X-Arg/Lys motifs and macrolides displaying a broader specificity, a structural basis for their context-specific action has been lacking. Here, we present structures of ribosomes arrested during the synthesis of an Arg-Leu-Arg sequence by the macrolide erythromycin (ERY) and the ketolide telithromycin (TEL). Together with deep mutagenesis and molecular dynamics simulations, the structures reveal how ERY and TEL interplay with the Arg-Leu-Arg motif to induce translational arrest and illuminate the basis for the less stringent sequence-specific action of ERY over TEL. Because programmed stalling at the Arg/Lys-X-Arg/Lys motifs is used to activate expression of antibiotic resistance genes, our study also provides important insights for future development of improved macrolide antibiotics.

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