4WF9

The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with telithromycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus.

Eyal, Z.Matzov, D.Krupkin, M.Wekselman, I.Paukner, S.Zimmerman, E.Rozenberg, H.Bashan, A.Yonath, A.

(2015) Proc Natl Acad Sci U S A 112: E5805-E5814

  • DOI: 10.1073/pnas.1517952112
  • Primary Citation of Related Structures:  
    4WCE, 4WFA, 4WFB, 4WF9

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel ada.yonath@weizmann.ac.il.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2A277Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplBSAOUHSC_02509
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore P60430 
Go to UniProtKB:  P60430
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3B220Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplCSAOUHSC_02512
Find proteins for Q2FW06 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FW06 
Go to UniProtKB:  Q2FW06
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4C207Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplDSAOUHSC_02511
Find proteins for Q2FW07 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FW07 
Go to UniProtKB:  Q2FW07
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5D179Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplESAOUHSC_02500
Find proteins for Q2FW18 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FW18 
Go to UniProtKB:  Q2FW18
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6E178Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplFSAOUHSC_02496
Find proteins for Q2FW21 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FW21 
Go to UniProtKB:  Q2FW21
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13G145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplMSAOUHSC_02478
Find proteins for Q2FW38 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FW38 
Go to UniProtKB:  Q2FW38
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14H122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplNSAOUHSC_02502
Find proteins for Q2FW16 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FW16 
Go to UniProtKB:  Q2FW16
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15I146Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplOSAOUHSC_02492
Find proteins for P0A0F8 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore P0A0F8 
Go to UniProtKB:  P0A0F8
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16J144Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplPSAOUHSC_02505
Find proteins for Q2FW13 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FW13 
Go to UniProtKB:  Q2FW13
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17K122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplQSAOUHSC_02484
Find proteins for Q2FW33 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FW33 
Go to UniProtKB:  Q2FW33
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18L119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplRSAOUHSC_02495
Find proteins for Q2FW22 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FW22 
Go to UniProtKB:  Q2FW22
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19M116Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplSSAOUHSC_01211
Find proteins for Q2FZ42 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FZ42 
Go to UniProtKB:  Q2FZ42
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20N118Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplTSAOUHSC_01784
Find proteins for Q2FXQ1 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FXQ1 
Go to UniProtKB:  Q2FXQ1
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21O102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplUSAOUHSC_01757
Find proteins for Q2FXS8 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FXS8 
Go to UniProtKB:  Q2FXS8
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22P117Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplVSAOUHSC_02507
Find proteins for Q2FW11 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FW11 
Go to UniProtKB:  Q2FW11
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23Q91Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplWSAOUHSC_02510
Find proteins for Q2FW08 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FW08 
Go to UniProtKB:  Q2FW08
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24R105Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplXSAOUHSC_02501
Find proteins for Q2FW17 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FW17 
Go to UniProtKB:  Q2FW17
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25S217Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
Gene Names: rplYctcSAUSA300_0479
Find proteins for Q2FJE0 (Staphylococcus aureus (strain USA300))
Explore Q2FJE0 
Go to UniProtKB:  Q2FJE0
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29V69Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmCSAOUHSC_02504
Find proteins for Q2FW14 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FW14 
Go to UniProtKB:  Q2FW14
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32Z58Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmFSAOUHSC_01078
Find proteins for Q2FZF1 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FZF1 
Go to UniProtKB:  Q2FZF1
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34245Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmHSAOUHSC_03055
Find proteins for Q2FUQ0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FUQ0 
Go to UniProtKB:  Q2FUQ0
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35366Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmISAOUHSC_01785
Find proteins for Q2FXQ0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FXQ0 
Go to UniProtKB:  Q2FXQ0
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27T94Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmASAOUHSC_01755
Find proteins for Q2FXT0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FXT0 
Go to UniProtKB:  Q2FXT0
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30W59Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmDSAOUHSC_02493
Find proteins for P0A0G2 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore P0A0G2 
Go to UniProtKB:  P0A0G2
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAX2923Staphylococcus aureus subsp. aureus NCTC 8325
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAY114Staphylococcus aureus subsp. aureus NCTC 8325
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TEL
Query on TEL

Download CCD File 
X
TELITHROMYCIN
C43 H65 N5 O10
LJVAJPDWBABPEJ-MMEUOAQYSA-N
 Ligand Interaction
EPE
Query on EPE

Download CCD File 
L
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SPD
Query on SPD

Download CCD File 
S, X
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download CCD File 
X
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
I, J, M, X, Y
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

Download CCD File 
X
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, G, O, R, T, X, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 282.66α = 90
b = 282.66β = 90
c = 877.075γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DNAdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-10-28
    Changes: Database references
  • Version 1.2: 2016-01-20
    Changes: Structure summary