1K9M image
Entry Detail
PDB ID:
1K9M
Keywords:
Title:
Co-crystal structure of tylosin bound to the 50S ribosomal subunit of Haloarcula marismortui
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2001-10-29
Release Date:
2002-07-19
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L37Ae
Chain IDs:AA (auth: 1)
Chain Length:73
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L37E
Chain IDs:BA (auth: 2)
Chain Length:56
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L39E
Chain IDs:CA (auth: 3)
Chain Length:48
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L44E
Chain IDs:DA (auth: 4)
Chain Length:92
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polyribonucleotide
Description:23S RRNA
Chain IDs:A
Chain Length:2922
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polyribonucleotide
Description:5S RRNA
Chain IDs:B
Chain Length:122
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L2
Chain IDs:C
Chain Length:239
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L3
Chain IDs:D
Chain Length:337
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L4
Chain IDs:E
Chain Length:246
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L5
Chain IDs:F
Chain Length:176
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L6
Chain IDs:G
Chain Length:177
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L7AE
Chain IDs:H
Chain Length:119
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L10
Chain IDs:I
Chain Length:348
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L10E
Chain IDs:J
Chain Length:167
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L13
Chain IDs:K
Chain Length:145
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L14
Chain IDs:L
Chain Length:132
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L15
Chain IDs:M
Chain Length:164
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L15E
Chain IDs:N
Chain Length:194
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L18
Chain IDs:O
Chain Length:186
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L18E
Chain IDs:P
Chain Length:115
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L19E
Chain IDs:Q
Chain Length:148
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L21E
Chain IDs:R
Chain Length:95
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L22
Chain IDs:S
Chain Length:154
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L23
Chain IDs:T
Chain Length:84
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L24
Chain IDs:U
Chain Length:119
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L24E
Chain IDs:V
Chain Length:66
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L29
Chain IDs:W
Chain Length:70
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L30
Chain IDs:X
Chain Length:154
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L31E
Chain IDs:Y
Chain Length:91
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Description:RIBOSOMAL PROTEIN L32E
Chain IDs:Z
Chain Length:240
Number of Molecules:1
Biological Source:Haloarcula marismortui
Primary Citation
The structures of four macrolide antibiotics bound to the large ribosomal subunit.
Mol.Cell 10 117 128 (2002)
PMID: 12150912 DOI: 10.1016/S1097-2765(02)00570-1

Abstact

Crystal structures of the Haloarcula marismortui large ribosomal subunit complexed with the 16-membered macrolide antibiotics carbomycin A, spiramycin, and tylosin and a 15-membered macrolide, azithromycin, show that they bind in the polypeptide exit tunnel adjacent to the peptidyl transferase center. Their location suggests that they inhibit protein synthesis by blocking the egress of nascent polypeptides. The saccharide branch attached to C5 of the lactone rings extends toward the peptidyl transferase center, and the isobutyrate extension of the carbomycin A disaccharide overlaps the A-site. Unexpectedly, a reversible covalent bond forms between the ethylaldehyde substituent at the C6 position of the 16-membered macrolides and the N6 of A2103 (A2062, E. coli). Mutations in 23S rRNA that result in clinical resistance render the binding site less complementary to macrolides.

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Primary Citation of related structures