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 

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Ligand Structure Quality Assessment 


This is version 1.3 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:  
    4WF9, 4WCE, 4WFA, 4WFB

  • 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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth A]277Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplBSAOUHSC_02509
UniProt
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth B]220Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplCSAOUHSC_02512
UniProt
Find proteins for Q2FW06 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth C]207Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplDSAOUHSC_02511
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth D]179Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplESAOUHSC_02500
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth E]178Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplFSAOUHSC_02496
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13H [auth G]145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplMSAOUHSC_02478
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14I [auth H]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplNSAOUHSC_02502
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15J [auth I]146Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplOSAOUHSC_02492
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16K [auth J]144Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplPSAOUHSC_02505
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17L [auth K]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplQSAOUHSC_02484
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18M [auth L]119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplRSAOUHSC_02495
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19N [auth M]116Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplSSAOUHSC_01211
UniProt
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20O [auth N]118Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplTSAOUHSC_01784
UniProt
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21P [auth O]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplUSAOUHSC_01757
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22Q [auth P]117Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplVSAOUHSC_02507
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23R [auth Q]91Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplWSAOUHSC_02510
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24S [auth R]105Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplXSAOUHSC_02501
UniProt
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25T [auth S]217Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
Gene Names: rplYctcSAUSA300_0479
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27U [auth T]94Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmASAOUHSC_01755
UniProt
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29V69Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmCSAOUHSC_02504
UniProt
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30W59Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmDSAOUHSC_02493
UniProt
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32X [auth Z]58Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmFSAOUHSC_01078
UniProt
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34Y [auth 2]45Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmHSAOUHSC_03055
UniProt
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35Z [auth 3]66Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmISAOUHSC_01785
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA [auth X]2923Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB [auth Y]114Staphylococcus aureus subsp. aureus NCTC 8325
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TEL (Subject of Investigation/LOI)
Query on TEL

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AA [auth X]TELITHROMYCIN
C43 H65 N5 O10
LJVAJPDWBABPEJ-PNUFFHFMSA-N
 Ligand Interaction
EPE
Query on EPE

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CP [auth L]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SPD
Query on SPD

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AO [auth X], GP [auth S], XN [auth X], YN [auth X], ZN [auth X]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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BA [auth X], CA [auth X], DA [auth X], EA [auth X], FA [auth X], GA [auth X], HA [auth X], IA [auth X](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
MN
Query on MN

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AC [auth X] , AD [auth X] , AE [auth X] , AF [auth X] , AH [auth X] , AI [auth X] , AK [auth X] , AP [auth I] , 
AC [auth X],  AD [auth X],  AE [auth X],  AF [auth X],  AH [auth X],  AI [auth X],  AK [auth X],  AP [auth I],  BC [auth X],  BD [auth X],  BE [auth X],  BF [auth X],  BG [auth X],  BH [auth X],  BI [auth X],  BJ [auth X],  BK [auth X],  BP [auth J],  CC [auth X],  CD [auth X],  CE [auth X],  CF [auth X],  CG [auth X],  CH [auth X],  CI [auth X],  CJ [auth X],  CK [auth X],  DC [auth X],  DD [auth X],  DE [auth X],  DF [auth X],  DG [auth X],  DH [auth X],  DI [auth X],  DJ [auth X],  DK [auth X],  DP [auth M],  EC [auth X],  ED [auth X],  EE [auth X],  EF [auth X],  EG [auth X],  EH [auth X],  EI [auth X],  EJ [auth X],  EK [auth X],  EO [auth X],  FB [auth X],  FC [auth X],  FD [auth X],  FE [auth X],  FF [auth X],  FG [auth X],  FH [auth X],  FI [auth X],  FJ [auth X],  FK [auth X],  FO [auth X],  GB [auth X],  GC [auth X],  GD [auth X],  GE [auth X],  GF [auth X],  GG [auth X],  GH [auth X],  GI [auth X],  GJ [auth X],  GK [auth X],  GO [auth X],  HB [auth X],  HC [auth X],  HD [auth X],  HE [auth X],  HF [auth X],  HG [auth X],  HH [auth X],  HI [auth X],  HJ [auth X],  HK [auth X],  IB [auth X],  IC [auth X],  ID [auth X],  IE [auth X],  IF [auth X],  IG [auth X],  II [auth X],  IJ [auth X],  IK [auth X],  IO [auth X],  JB [auth X],  JC [auth X],  JD [auth X],  JE [auth X],  JF [auth X],  JG [auth X],  JI [auth X],  JJ [auth X],  JK [auth X],  JO [auth Y],  KB [auth X],  KC [auth X],  KD [auth X],  KE [auth X],  KF [auth X],  KG [auth X],  KI [auth X],  KJ [auth X],  KK [auth X],  KO [auth Y],  LB [auth X],  LC [auth X],  LD [auth X],  LE [auth X],  LF [auth X],  LG [auth X],  LI [auth X],  LJ [auth X],  LK [auth X],  MB [auth X],  MC [auth X],  MD [auth X],  ME [auth X],  MF [auth X],  MG [auth X],  MI [auth X],  MJ [auth X],  MO [auth Y],  NB [auth X],  NC [auth X],  ND [auth X],  NE [auth X],  NF [auth X],  NG [auth X],  NI [auth X],  NJ [auth X],  NO [auth Y],  OB [auth X],  OC [auth X],  OD [auth X],  OE [auth X],  OF [auth X],  OG [auth X],  PB [auth X],  PC [auth X],  PD [auth X],  PE [auth X],  PF [auth X],  PG [auth X],  PH [auth X],  PM [auth X],  QB [auth X],  QC [auth X],  QD [auth X],  QE [auth X],  QF [auth X],  QG [auth X],  QH [auth X],  QM [auth X],  QN [auth X],  QO [auth Y],  RB [auth X],  RC [auth X],  RD [auth X],  RE [auth X],  RF [auth X],  RG [auth X],  RH [auth X],  RM [auth X],  RN [auth X],  SB [auth X],  SC [auth X],  SD [auth X],  SE [auth X],  SF [auth X],  SG [auth X],  SH [auth X],  SI [auth X],  SM [auth X],  SO [auth Y],  TB [auth X],  TC [auth X],  TD [auth X],  TE [auth X],  TF [auth X],  TG [auth X],  TH [auth X],  TJ [auth X],  TM [auth X],  UB [auth X],  UC [auth X],  UD [auth X],  UE [auth X],  UF [auth X],  UG [auth X],  UH [auth X],  VB [auth X],  VC [auth X],  VD [auth X],  VE [auth X],  VF [auth X],  VG [auth X],  VH [auth X],  VJ [auth X],  WB [auth X],  WC [auth X],  WD [auth X],  WE [auth X],  WF [auth X],  WG [auth X],  WH [auth X],  WN [auth X],  XB [auth X],  XC [auth X],  XD [auth X],  XE [auth X],  XF [auth X],  XG [auth X],  XH [auth X],  YB [auth X],  YC [auth X],  YD [auth X],  YE [auth X],  YG [auth X],  YH [auth X],  ZB [auth X],  ZC [auth X],  ZD [auth X],  ZE [auth X],  ZG [auth X],  ZH [auth X],  ZO [auth I]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

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BO [auth X], CO [auth X], DO [auth X]ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AB [auth X] , AG [auth X] , AJ [auth X] , AL [auth X] , AM [auth X] , AN [auth X] , BB [auth X] , BL [auth X] , 
AB [auth X],  AG [auth X],  AJ [auth X],  AL [auth X],  AM [auth X],  AN [auth X],  BB [auth X],  BL [auth X],  BM [auth X],  BN [auth X],  CB [auth X],  CL [auth X],  CM [auth X],  CN [auth X],  DB [auth X],  DL [auth X],  DM [auth X],  DN [auth X],  EB [auth X],  EL [auth X],  EM [auth X],  EN [auth X],  EP [auth O],  FL [auth X],  FM [auth X],  FN [auth X],  FP [auth R],  GL [auth X],  GM [auth X],  GN [auth X],  HL [auth X],  HM [auth X],  HN [auth X],  HO [auth X],  HP [auth T],  IH [auth X],  IL [auth X],  IM [auth X],  IN [auth X],  JA [auth X],  JH [auth X],  JL [auth X],  JM [auth X],  JN [auth X],  KA [auth X],  KH [auth X],  KL [auth X],  KM [auth X],  KN [auth X],  LA [auth X],  LH [auth X],  LL [auth X],  LM [auth X],  LN [auth X],  LO [auth Y],  MA [auth X],  MH [auth X],  MK [auth X],  ML [auth X],  MM [auth X],  MN [auth X],  NA [auth X],  NH [auth X],  NK [auth X],  NL [auth X],  NM [auth X],  NN [auth X],  OA [auth X],  OH [auth X],  OI [auth X],  OJ [auth X],  OK [auth X],  OL [auth X],  OM [auth X],  ON [auth X],  OO [auth Y],  PA [auth X],  PI [auth X],  PJ [auth X],  PK [auth X],  PL [auth X],  PN [auth X],  PO [auth Y],  QA [auth X],  QI [auth X],  QJ [auth X],  QK [auth X],  QL [auth X],  RA [auth X],  RI [auth X],  RJ [auth X],  RK [auth X],  RL [auth X],  RO [auth Y],  SA [auth X],  SJ [auth X],  SK [auth X],  SL [auth X],  SN [auth X],  TA [auth X],  TI [auth X],  TK [auth X],  TL [auth X],  TN [auth X],  TO [auth A],  UA [auth X],  UI [auth X],  UJ [auth X],  UK [auth X],  UL [auth X],  UM [auth X],  UN [auth X],  UO [auth B],  VA [auth X],  VI [auth X],  VK [auth X],  VL [auth X],  VM [auth X],  VN [auth X],  VO [auth C],  WA [auth X],  WI [auth X],  WJ [auth X],  WK [auth X],  WL [auth X],  WM [auth X],  WO [auth C],  XA [auth X],  XI [auth X],  XJ [auth X],  XK [auth X],  XL [auth X],  XM [auth X],  XO [auth C],  YA [auth X],  YF [auth X],  YI [auth X],  YJ [auth X],  YK [auth X],  YL [auth X],  YM [auth X],  YO [auth G],  ZA [auth X],  ZF [auth X],  ZI [auth X],  ZJ [auth X],  ZK [auth X],  ZL [auth X],  ZM [auth X]
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

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2021-01-27
    Changes: Data collection, Derived calculations, Structure summary