1NJP

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.244 

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This is version 1.2 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: 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 ...

    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
MoleculeChainsSequence 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 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Go to UniProtKB:  Q9RXJ5
Entity Groups  
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UniProt GroupQ9RXJ5
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Entity ID: 4
MoleculeChainsSequence 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 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Explore Q9RX88 
Go to UniProtKB:  Q9RX88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RX88
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA [auth 0]2,880Deinococcus radiodurans
Protein Feature View
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Entity ID: 2
MoleculeChainsLengthOrganismImage
tRNA acceptor stem mimicB [auth 5]35N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.244 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.9α = 90
b = 409.9β = 90
c = 695.9γ = 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