3PIP

Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 

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Literature

Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.

Belousoff, M.J.Shapira, T.Bashan, A.Zimmerman, E.Rozenberg, H.Arakawa, K.Kinashi, H.Yonath, A.

(2011) Proc Natl Acad Sci U S A 108: 2717-2722

  • DOI: 10.1073/pnas.1019406108
  • Primary Citation of Related Structures:  
    3PIO, 3PIP

  • PubMed Abstract: 
  • The structures of the large ribosomal subunit of Deinococcus radiodurans (D50S) in complex with the antibiotic lankamycin (3.2 Å) and a double antibiotic complex of lankamycin and lankacidin C (3.45 Å) have been determined, in continuation of previous crystallographic studies on lankacidin-D50S complex ...

    The structures of the large ribosomal subunit of Deinococcus radiodurans (D50S) in complex with the antibiotic lankamycin (3.2 Å) and a double antibiotic complex of lankamycin and lankacidin C (3.45 Å) have been determined, in continuation of previous crystallographic studies on lankacidin-D50S complex. These two drugs have been previously reported to inhibit ribosomal function with mild synergistic effect. Lankamycin, a member of the macrolide family, binds in a similar manner to erythromycin. However, when in complex with lankacidin, lankamycin is located so that it can form interactions with lankacidin in the adjacent ribosomal binding site. When compared to the well-documented synergistic antibiotics, Streptogramins A and B, the pair of lankacidin and lankamycin bind in similar sites, the peptidyl transferase center and nascent peptide exit tunnel, respectively. Herein, we discuss the structural basis for antibiotic synergism and highlight the key factors involved in ribosomal inhibition.


    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth A]274Deinococcus radioduransMutation(s): 0 
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Entity ID: 4
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50S ribosomal protein L3D [auth B]211Deinococcus radioduransMutation(s): 0 
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Entity ID: 5
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50S ribosomal protein L4E [auth C]205Deinococcus radioduransMutation(s): 0 
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Entity ID: 6
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50S ribosomal protein L5F [auth D]180Deinococcus radioduransMutation(s): 0 
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Entity ID: 7
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50S ribosomal protein L6G [auth E]185Deinococcus radioduransMutation(s): 0 
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Entity ID: 8
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50S ribosomal protein L11H [auth F]144Deinococcus radioduransMutation(s): 0 
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Entity ID: 9
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50S ribosomal protein L13I [auth G]174Deinococcus radioduransMutation(s): 0 
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Entity ID: 10
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50S ribosomal protein L14J [auth H]134Deinococcus radioduransMutation(s): 0 
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Entity ID: 11
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50S ribosomal protein L15K [auth I]156Deinococcus radioduransMutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L16L [auth J]141Deinococcus radioduransMutation(s): 0 
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Entity ID: 13
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50S ribosomal protein L17M [auth K]116Deinococcus radioduransMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L18N [auth L]114Deinococcus radioduransMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L19O [auth M]166Deinococcus radioduransMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L20P [auth N]118Deinococcus radioduransMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L21Q [auth O]100Deinococcus radioduransMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L22R [auth P]134Deinococcus radioduransMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L23S [auth Q]95Deinococcus radioduransMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L24T [auth R]115Deinococcus radioduransMutation(s): 0 
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Entity ID: 21
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50S ribosomal protein L25U [auth S]237Deinococcus radioduransMutation(s): 0 
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Find proteins for Q9RX88 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 22
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50S ribosomal protein L27V [auth T]91Deinococcus radioduransMutation(s): 0 
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Entity ID: 23
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50S ribosomal protein L28W [auth U]81Deinococcus radioduransMutation(s): 0 
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Find proteins for Q9RRG8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 24
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50S ribosomal protein L29X [auth V]67Deinococcus radioduransMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L30Y [auth W]55Deinococcus radioduransMutation(s): 0 
UniProt
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Entity ID: 26
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50S ribosomal protein L32Z60Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for P49228 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 27
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50S ribosomal protein L33AA [auth 1]55Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSS4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 28
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50S ribosomal protein L34BA [auth 2]47Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSH2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 29
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50S ribosomal protein L35CA [auth 3]66Deinococcus radioduransMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L36DA [auth 4]37Deinococcus radioduransMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
RIBOSOMAL 23S RNAA [auth X]2880Deinococcus radiodurans R1
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB [auth Y]123Deinococcus radiodurans R1
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMA (Subject of Investigation/LOI)
Query on LMA

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FA [auth X]Lankamycin
C43 H74 O15
FIYJFVCGASKYLV-QDYGBMDYSA-N
 Ligand Interaction
LC2 (Subject of Investigation/LOI)
Query on LC2

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EA [auth X]N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide
C25 H33 N O7
ATDILMLBOZKFGI-JUTMVFGESA-N
 Ligand Interaction
K
Query on K

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AD [auth X], BD [auth X], CD [auth X], ZC [auth X]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AB [auth X] , AC [auth X] , BB [auth X] , BC [auth X] , CB [auth X] , CC [auth X] , DB [auth X] , DC [auth X] , 
AB [auth X],  AC [auth X],  BB [auth X],  BC [auth X],  CB [auth X],  CC [auth X],  DB [auth X],  DC [auth X],  EB [auth X],  EC [auth X],  FB [auth X],  FC [auth X],  GA [auth X],  GB [auth X],  GC [auth X],  HA [auth X],  HB [auth X],  HC [auth X],  IA [auth X],  IB [auth X],  IC [auth X],  ID [auth I],  JA [auth X],  JB [auth X],  JC [auth X],  JD [auth U],  KA [auth X],  KB [auth X],  KC [auth X],  LA [auth X],  LB [auth X],  LC [auth X],  MA [auth X],  MB [auth X],  MC [auth X],  NA [auth X],  NB [auth X],  NC [auth X],  OA [auth X],  OB [auth X],  OC [auth X],  PA [auth X],  PB [auth X],  PC [auth X],  QA [auth X],  QB [auth X],  QC [auth X],  RA [auth X],  RB [auth X],  RC [auth X],  SA [auth X],  SB [auth X],  SC [auth X],  TA [auth X],  TB [auth X],  TC [auth X],  UA [auth X],  UB [auth X],  UC [auth X],  VA [auth X],  VB [auth X],  VC [auth X],  WA [auth X],  WB [auth X],  WC [auth X],  XA [auth X],  XB [auth X],  XC [auth X],  YA [auth X],  YB [auth X],  YC [auth X],  ZA [auth X],  ZB [auth X]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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DD [auth X], ED [auth X], FD [auth X], GD [auth X], HD [auth X]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.723α = 90
b = 408.562β = 90
c = 693.334γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance