1NJN

The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with the antibiotic sparsomycin

• PDB DOI: https://doi.org/10.2210/pdb1NJN/pdb
• NAKB: 1NJN

• Classification: RIBOSOME
• Organism(s): Deinococcus radiodurans
• Mutation(s): No 


• Deposited: 2003-01-02 Released: 2003-02-11 
• Deposition Author(s): Bashan, A., Agmon, I., Zarivatch, R., Schluenzen, F., Harms, J.M., Berisio, R., Bartels, H., Hansen, H.A., Yonath, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 0.308 
• R-Value Work: 0.284 
• R-Value Observed: 0.284 

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

• PubMed: 12535524 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 933.77 kDa 
• Atom Count: 59,381 
• Modelled Residue Count: 2,766 
• Deposited Residue Count: 2,880 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
23S ribosomal RNA	A [auth 0]	2,880	Deinococcus radiodurans

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPS	B [auth 0]	SPARSOMYCIN C13 H19 N3 O5 S2 XKLZIVIOZDNKEQ-CLQLPEFOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 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 = 169.1	α = 90
b = 409.9	β = 90
c = 696.3	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CCP4	phasing
O	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-11 
Deposition Author(s): Bashan, A., Agmon, I., Zarivatch, R., Schluenzen, F., Harms, J.M., Berisio, R., Bartels, H., Hansen, H.A., Yonath, A.

Revision History  

• 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