1NJM

The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.284 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of the ribosomal machinery for Peptide bond formation, translocation, and nascent chain progression

Bashan, A.Agmon, I.Zarivatch, R.Schluenzen, F.Harms, J.M.Berisio, R.Bartels, H.Franceschi, F.Auerbach, T.Hansen, H.A.Kossoy, E.Kessler, M.Yonath, A.

(2003) Mol Cell 11: 91-102

  • DOI: https://doi.org/10.1016/s1097-2765(03)00009-1
  • Primary Citation of Related Structures:  
    1NJM, 1NJN, 1NJO, 1NJP

  • PubMed Abstract: 

    Crystal structures of tRNA mimics complexed with the large ribosomal subunit of Deinococcus radiodurans indicate that remote interactions determine the precise orientation of tRNA in the peptidyl-transferase center (PTC). The PTC tolerates various orientations of puromycin derivatives and its flexibility allows the conformational rearrangements required for peptide-bond formation. Sparsomycin binds to A2602 and alters the PTC conformation. H69, the intersubunit-bridge connecting the PTC and decoding site, may also participate in tRNA placement and translocation. A spiral rotation of the 3' end of the A-site tRNA around a 2-fold axis of symmetry identified within the PTC suggests a unified ribosomal machinery for peptide-bond formation, A-to-P-site translocation, and entrance of nascent proteins into the exit tunnel. Similar 2-fold related regions, detected in all known structures of large ribosomal subunits, indicate the universality of this mechanism.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16C [auth K]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))
Explore Q9RXJ5 
Go to UniProtKB:  Q9RXJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RXJ5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
GENERAL STRESS PROTEIN CTCD [auth T]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))
Explore Q9RX88 
Go to UniProtKB:  Q9RX88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RX88
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth 0]2,880Deinococcus radiodurans
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
tRNA acceptor stem mimicB [auth 5]35N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPS
Query on SPS

Download Ideal Coordinates CCD File 
E [auth 0]SPARSOMYCIN
C13 H19 N3 O5 S2
XKLZIVIOZDNKEQ-CLQLPEFOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.284 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.6α = 90
b = 409.4β = 90
c = 695.1γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
CNSrefinement
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description