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 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth A]274Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXJ9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth B]211Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXK2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth C]205Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXK1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth D]180Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXJ0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth E]185Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSL3 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11H [auth F]144Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSS7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13I [auth G]174Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXY1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14J [auth H]134Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXJ2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15K [auth I]156Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSK9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16L [auth J]141Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXJ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17M [auth K]116Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSJ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18N [auth L]114Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSL2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19O [auth M]166Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RWB4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20P [auth N]118Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSW7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21Q [auth O]100Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RY64 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22R [auth P]134Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXJ7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23S [auth Q]95Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXK0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24T [auth R]115Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXJ1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25U [auth S]237Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RX88 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27V [auth T]91Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RY65 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28W [auth U]81Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RRG8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29X [auth V]67Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXJ4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30Y [auth W]55Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSL0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3260Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for P49228 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AA [auth 1]55Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSS4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BA [auth 2]47Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSH2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CA [auth 3]66Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSW6 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36DA [auth 4]37Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RSK0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 1
MoleculeChains LengthOrganismImage
RIBOSOMAL 23S RNAA [auth X]2,880Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth Y]123Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMA
Query on LMA

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FA [auth X]Lankamycin
C43 H74 O15
FIYJFVCGASKYLV-QDYGBMDYSA-N
LC2
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
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
MG
Query on MG

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AB [auth X]
AC [auth X]
BB [auth X]
BC [auth X]
CB [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
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
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
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.3: 2024-10-09
    Changes: Structure summary