2OGO

The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative retapamulin (SB-275833)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.66 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity.

Davidovich, C.Bashan, A.Auerbach-Nevo, T.Yaggie, R.D.Gontarek, R.R.Yonath, A.

(2007) Proc Natl Acad Sci U S A 104: 4291-4296

  • DOI: https://doi.org/10.1073/pnas.0700041104
  • Primary Citation of Related Structures:  
    2OGM, 2OGN, 2OGO

  • PubMed Abstract: 

    New insights into functional flexibility at the peptidyl transferase center (PTC) and its vicinity were obtained by analysis of pleuromutilins binding modes to the ribosome. The crystal structures of Deinococcus radiodurans large ribosomal subunit complexed with each of three pleuromutilin derivatives: retapamulin (SB-275833), SB-280080, and SB-571519, show that all bind to the PTC with their core oriented similarly at the A-site and their C14 extensions pointing toward the P-site. Except for an H-bond network with a single nucleotide, G2061, which involves the essential keto group of all three compounds, only minor hydrophobic contacts are formed between the pleuromutilin C14 extensions and any ribosomal component, consistent with the PTC tolerance to amino acid diversity. Efficient drug binding mode is attained by a mechanism based on induced-fit motions exploiting the ribosomal intrinsic functional flexibility and resulting in conformational rearrangements that seal the pleuromutilin-binding pocket and tightens it up. Comparative studies identified a network of remote interactions around the PTC, indicating that pleuromutilins selectivity is acquired by nonconserved nucleotides residing in the PTC vicinity, in a fashion resembling allosterism. Likewise, pleuromutilin resistant mechanisms involve nucleotides residing in the environs of the binding pocket, consistent with their slow resistance-development rates.


  • Organizational Affiliation

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


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3211Deinococcus 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))
Explore Q9RXK2 
Go to UniProtKB:  Q9RXK2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RXK2
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth 0]2,880Deinococcus radiodurans
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G34
Query on G34

Download Ideal Coordinates CCD File 
C [auth 0]Retapamulin
C30 H47 N O4 S
STZYTFJPGGDRJD-NHUWBDDWSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.66 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.260 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.115α = 90
b = 405.873β = 90
c = 695.243γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Structure summary