1YHQ

Crystal Structure Of Azithromycin Bound To The G2099A Mutant 50S Ribosomal Subunit Of Haloarcula Marismortui


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance.

Tu, D.Blaha, G.Moore, P.B.Steitz, T.A.

(2005) Cell 121: 257-270

  • DOI: 10.1016/j.cell.2005.02.005
  • Primary Citation of Related Structures:  
    1YHQ, 1YI2, 1YJ9, 1YIT, 1YIJ, 1YJW, 1YJN

  • PubMed Abstract: 
  • Crystal structures of H. marismortui large ribosomal subunits containing the mutation G2099A (A2058 in E. coli) with erythromycin, azithromycin, clindamycin, virginiamycin S, and telithromycin bound explain why eubacterial ribosomes containing the mutation A2058G are resistant to them ...

    Crystal structures of H. marismortui large ribosomal subunits containing the mutation G2099A (A2058 in E. coli) with erythromycin, azithromycin, clindamycin, virginiamycin S, and telithromycin bound explain why eubacterial ribosomes containing the mutation A2058G are resistant to them. Azithromycin binds almost identically to both G2099A and wild-type subunits, but the erythromycin affinity increases by more than 10(4)-fold, implying that desolvation of the N2 of G2099 accounts for the low wild-type affinity for macrolides. All macrolides bind similarly to the H. marismortui subunit, but their binding differs significantly from what has been reported in the D. radioidurans subunit. The synergy in the binding of streptogramins A and B appears to result from a reorientation of the base of A2103 (A2062, E. coli) that stacks between them. The structure of large subunit containing a three residue deletion mutant of L22 shows a change in the L22 structure and exit tunnel shape that illuminates its macrolide resistance phenotype.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2PC [auth A]240Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3PD [auth B]338Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4EE [auth C]246Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5PF [auth D]177Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6PG [auth E]178Haloarcula marismortuiMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AEH [auth F]120Haloarcula marismortuiMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOGI [auth G]348Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L10EJ [auth H]177Haloarcula marismortuiMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L11PK [auth I]162Haloarcula marismortuiMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13PL [auth J]145Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14PM [auth K]132Haloarcula marismortuiMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15PN [auth L]165Haloarcula marismortuiMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal Protein L15EO [auth M]194Haloarcula marismortuiMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18PP [auth N]187Haloarcula marismortuiMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L18eQ [auth O]116Haloarcula marismortuiMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L19ER [auth P]149Haloarcula marismortuiMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L21eS [auth Q]96Haloarcula marismortuiMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L22PT [auth R]155Haloarcula marismortuiMutation(s): 0 
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Entity ID: 21
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50S ribosomal protein L23PU [auth S]85Haloarcula marismortuiMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24PV [auth T]120Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24EW [auth U]66Haloarcula marismortuiMutation(s): 0 
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Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29PX [auth V]71Haloarcula marismortuiMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30PY [auth W]154Haloarcula marismortuiMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31eZ [auth X]92Haloarcula marismortuiMutation(s): 0 
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Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32EAA [auth Y]241Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37AeBA [auth Z]83Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37eCA [auth 1]57Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L39eDA [auth 2]50Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L44EEA [auth 3]92Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S Ribosomal RNAA [auth 0]2922Haloarcula marismortui
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S Ribosomal RNAB [auth 9]122Haloarcula marismortui
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Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZIT
Query on ZIT

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FA [auth 0]AZITHROMYCIN
C38 H72 N2 O12
MQTOSJVFKKJCRP-BICOPXKESA-N
 Ligand Interaction
CD
Query on CD

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FL [auth O], PL [auth U], SL [auth Z], TL [auth 1], WL [auth 3]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

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AH [auth 0] , AI [auth 0] , AJ [auth 0] , AK [auth 0] , BH [auth 0] , BI [auth 0] , BJ [auth 0] , BK [auth 0] , 
AH [auth 0],  AI [auth 0],  AJ [auth 0],  AK [auth 0],  BH [auth 0],  BI [auth 0],  BJ [auth 0],  BK [auth 0],  CH [auth 0],  CI [auth 0],  CJ [auth 0],  CK [auth 0],  DH [auth 0],  DI [auth 0],  DJ [auth 0],  EH [auth 0],  EI [auth 0],  EJ [auth 0],  FH [auth 0],  FI [auth 0],  FJ [auth 0],  GH [auth 0],  GI [auth 0],  GJ [auth 0],  GK [auth 9],  HH [auth 0],  HI [auth 0],  HJ [auth 0],  HK [auth 9],  IH [auth 0],  II [auth 0],  IJ [auth 0],  JH [auth 0],  JI [auth 0],  JJ [auth 0],  KH [auth 0],  KI [auth 0],  KJ [auth 0],  LH [auth 0],  LI [auth 0],  LJ [auth 0],  LK [auth A],  LL [auth R],  MH [auth 0],  MI [auth 0],  MJ [auth 0],  MK [auth A],  NG [auth 0],  NH [auth 0],  NI [auth 0],  NJ [auth 0],  NK [auth A],  NL [auth S],  OG [auth 0],  OH [auth 0],  OI [auth 0],  OJ [auth 0],  PG [auth 0],  PH [auth 0],  PI [auth 0],  PJ [auth 0],  QG [auth 0],  QH [auth 0],  QI [auth 0],  QJ [auth 0],  QK [auth B],  RG [auth 0],  RH [auth 0],  RI [auth 0],  RJ [auth 0],  RK [auth B],  SG [auth 0],  SH [auth 0],  SI [auth 0],  SJ [auth 0],  TG [auth 0],  TH [auth 0],  TI [auth 0],  TJ [auth 0],  TK [auth F],  UG [auth 0],  UH [auth 0],  UI [auth 0],  UJ [auth 0],  UL [auth 1],  VG [auth 0],  VH [auth 0],  VI [auth 0],  VJ [auth 0],  VK [auth H],  VL [auth 1],  WG [auth 0],  WH [auth 0],  WI [auth 0],  WJ [auth 0],  XG [auth 0],  XH [auth 0],  XI [auth 0],  XJ [auth 0],  YG [auth 0],  YH [auth 0],  YI [auth 0],  YJ [auth 0],  YL [auth 3],  ZG [auth 0],  ZH [auth 0],  ZI [auth 0],  ZJ [auth 0]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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OD [auth 0], PD [auth 0]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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BL [auth L] , DG [auth 0] , DL [auth M] , EG [auth 0] , EL [auth N] , FG [auth 0] , GG [auth 0] , GL [auth O] , 
BL [auth L],  DG [auth 0],  DL [auth M],  EG [auth 0],  EL [auth N],  FG [auth 0],  GG [auth 0],  GL [auth O],  HG [auth 0],  IG [auth 0],  JG [auth 0],  KG [auth 0],  KK [auth A],  KL [auth R],  LG [auth 0],  MG [auth 0],  PK [auth B],  RL [auth Y],  XK [auth J],  XL [auth 3],  YK [auth J],  ZK [auth J]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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AB [auth 0] , AC [auth 0] , AD [auth 0] , AL [auth K] , BB [auth 0] , BC [auth 0] , BD [auth 0] , CB [auth 0] , 
AB [auth 0],  AC [auth 0],  AD [auth 0],  AL [auth K],  BB [auth 0],  BC [auth 0],  BD [auth 0],  CB [auth 0],  CC [auth 0],  CD [auth 0],  DB [auth 0],  DC [auth 0],  DD [auth 0],  DK [auth 9],  EB [auth 0],  EC [auth 0],  ED [auth 0],  FB [auth 0],  FC [auth 0],  FD [auth 0],  GA [auth 0],  GB [auth 0],  GC [auth 0],  GD [auth 0],  HA [auth 0],  HB [auth 0],  HC [auth 0],  HD [auth 0],  IA [auth 0],  IB [auth 0],  IC [auth 0],  ID [auth 0],  IK [auth A],  JA [auth 0],  JB [auth 0],  JC [auth 0],  JD [auth 0],  JK [auth A],  KA [auth 0],  KB [auth 0],  KC [auth 0],  KD [auth 0],  LA [auth 0],  LB [auth 0],  LC [auth 0],  LD [auth 0],  MA [auth 0],  MB [auth 0],  MC [auth 0],  MD [auth 0],  NA [auth 0],  NB [auth 0],  NC [auth 0],  ND [auth 0],  OA [auth 0],  OB [auth 0],  OC [auth 0],  OK [auth B],  OL [auth T],  PA [auth 0],  PB [auth 0],  PC [auth 0],  QA [auth 0],  QB [auth 0],  QC [auth 0],  QL [auth Y],  RA [auth 0],  RB [auth 0],  RC [auth 0],  SA [auth 0],  SB [auth 0],  SC [auth 0],  TA [auth 0],  TB [auth 0],  TC [auth 0],  UA [auth 0],  UB [auth 0],  UC [auth 0],  VA [auth 0],  VB [auth 0],  VC [auth 0],  WA [auth 0],  WB [auth 0],  WC [auth 0],  XA [auth 0],  XB [auth 0],  XC [auth 0],  YA [auth 0],  YB [auth 0],  YC [auth 0],  ZA [auth 0],  ZB [auth 0],  ZC [auth 0]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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AE [auth 0] , AF [auth 0] , AG [auth 0] , BE [auth 0] , BF [auth 0] , BG [auth 0] , CE [auth 0] , CF [auth 0] , 
AE [auth 0],  AF [auth 0],  AG [auth 0],  BE [auth 0],  BF [auth 0],  BG [auth 0],  CE [auth 0],  CF [auth 0],  CG [auth 0],  CL [auth M],  DE [auth 0],  DF [auth 0],  EE [auth 0],  EF [auth 0],  EK [auth 9],  FE [auth 0],  FF [auth 0],  FK [auth 9],  GE [auth 0],  GF [auth 0],  HE [auth 0],  HF [auth 0],  HL [auth Q],  IE [auth 0],  IF [auth 0],  IL [auth R],  JE [auth 0],  JF [auth 0],  JL [auth R],  KE [auth 0],  KF [auth 0],  LE [auth 0],  LF [auth 0],  ME [auth 0],  MF [auth 0],  ML [auth S],  NE [auth 0],  NF [auth 0],  OE [auth 0],  OF [auth 0],  PE [auth 0],  PF [auth 0],  QD [auth 0],  QE [auth 0],  QF [auth 0],  RD [auth 0],  RE [auth 0],  RF [auth 0],  SD [auth 0],  SE [auth 0],  SF [auth 0],  SK [auth C],  TD [auth 0],  TE [auth 0],  TF [auth 0],  UD [auth 0],  UE [auth 0],  UF [auth 0],  UK [auth H],  VD [auth 0],  VE [auth 0],  VF [auth 0],  WD [auth 0],  WE [auth 0],  WF [auth 0],  WK [auth J],  XD [auth 0],  XE [auth 0],  XF [auth 0],  YD [auth 0],  YE [auth 0],  YF [auth 0],  ZD [auth 0],  ZE [auth 0],  ZF [auth 0]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.081α = 90
b = 298.91β = 90
c = 574.815γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance