7A0S image
Entry Detail
PDB ID:
7A0S
Keywords:
Title:
50S Deinococcus radiodurans ribosome bounded with mycinamicin I
Biological Source:
PDB Version:
Deposition Date:
2020-08-10
Release Date:
2021-08-18
Method Details:
Experimental Method:
Resolution:
3.22 Å
R-Value Free:
0.25
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
I 2 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:Z (auth: 1)
Chain Length:49
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:AA (auth: 2)
Chain Length:47
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:BA (auth: 3)
Chain Length:63
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:C (auth: A)
Chain Length:274
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:D (auth: B)
Chain Length:206
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:E (auth: C)
Chain Length:205
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:F (auth: D)
Chain Length:177
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:G (auth: E)
Chain Length:171
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:H (auth: G)
Chain Length:143
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:I (auth: H)
Chain Length:134
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:J (auth: I)
Chain Length:137
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:K (auth: J)
Chain Length:136
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:L (auth: K)
Chain Length:116
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:M (auth: L)
Chain Length:104
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:N (auth: M)
Chain Length:166
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:O (auth: N)
Chain Length:117
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:P (auth: O)
Chain Length:98
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:Q (auth: P)
Chain Length:134
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:R (auth: Q)
Chain Length:93
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:S (auth: R)
Chain Length:110
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:T (auth: S)
Chain Length:175
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:U (auth: T)
Chain Length:91
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:V (auth: U)
Chain Length:74
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:W (auth: V)
Chain Length:61
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:X (auth: W)
Chain Length:55
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polyribonucleotide
Description:RNA (2732-MER)
Chain IDs:A (auth: X)
Chain Length:2880
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polyribonucleotide
Description:RNA (122-MER)
Chain IDs:B (auth: Y)
Chain Length:123
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:Y (auth: Z)
Chain Length:58
Number of Molecules:1
Biological Source:Deinococcus radiodurans R1
Primary Citation
Ribosome-binding and anti-microbial studies of the mycinamicins, 16-membered macrolide antibiotics from Micromonospora griseorubida.
Nucleic Acids Res. 49 9560 9573 (2021)
PMID: 34417608 DOI: 10.1093/nar/gkab684

Abstact

Macrolides have been effective clinical antibiotics for over 70 years. They inhibit protein biosynthesis in bacterial pathogens by narrowing the nascent protein exit tunnel in the ribosome. The macrolide class of natural products consist of a macrolactone ring linked to one or more sugar molecules. Most of the macrolides used currently are semi-synthetic erythromycin derivatives, composed of a 14- or 15-membered macrolactone ring. Rapidly emerging resistance in bacterial pathogens is among the most urgent global health challenges, which render many antibiotics ineffective, including next-generation macrolides. To address this threat and advance a longer-term plan for developing new antibiotics, we demonstrate how 16-membered macrolides overcome erythromycin resistance in clinically isolated Staphylococcus aureus strains. By determining the structures of complexes of the large ribosomal subunit of Deinococcus radiodurans (D50S) with these 16-membered selected macrolides, and performing anti-microbial studies, we identified resistance mechanisms they may overcome. This new information provides important insights toward the rational design of therapeutics that are effective against drug resistant human pathogens.

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Primary Citation of related structures