4WF9 image
Deposition Date 2014-09-14
Release Date 2015-10-21
Last Version Date 2024-01-10
Entry Detail
PDB ID:
4WF9
Keywords:
Title:
The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with telithromycin
Biological Source:
Method Details:
Experimental Method:
Resolution:
3.43 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 65 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:Y (auth: 2)
Chain Length:45
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:Z (auth: 3)
Chain Length:66
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C (auth: A)
Chain Length:277
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D (auth: B)
Chain Length:220
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E (auth: C)
Chain Length:207
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:F (auth: D)
Chain Length:179
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:G (auth: E)
Chain Length:178
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:H (auth: G)
Chain Length:145
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:I (auth: H)
Chain Length:122
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:J (auth: I)
Chain Length:146
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:K (auth: J)
Chain Length:144
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:L (auth: K)
Chain Length:122
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:M (auth: L)
Chain Length:119
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:N (auth: M)
Chain Length:116
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:O (auth: N)
Chain Length:118
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:P (auth: O)
Chain Length:102
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:Q (auth: P)
Chain Length:117
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:R (auth: Q)
Chain Length:91
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:S (auth: R)
Chain Length:105
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:T (auth: S)
Chain Length:217
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain USA300)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:U (auth: T)
Chain Length:94
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:V
Chain Length:69
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:W
Chain Length:59
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:A (auth: X)
Chain Length:2923
Number of Molecules:1
Biological Source:Staphylococcus aureus subsp. aureus NCTC 8325
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: Y)
Chain Length:114
Number of Molecules:1
Biological Source:Staphylococcus aureus subsp. aureus NCTC 8325
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:X (auth: Z)
Chain Length:58
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Primary Citation
Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus.
Proc.Natl.Acad.Sci.USA 112 E5805 E5814 (2015)
PMID: 26464510 DOI: 10.1073/pnas.1517952112

Abstact

The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus.

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