Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 986.34 kDa 
• Atom Count: 60249 
• Residue Count: 3138 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

1NJP

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

• DOI: 10.2210/pdb1NJP/pdb
• NDB: RR0066

• 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: 3.50 Å
• R-Value Free: 0.295 
• R-Value Work: 0.244 
• R-Value Observed: 0.244 

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


• 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.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	K	141	Deinococcus radiodurans	Mutation(s): 0
Find proteins for Q9RXJ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Explore Q9RXJ5  Go to UniProtKB:  Q9RXJ5

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
GENERAL STRESS PROTEIN CTC	T	237	Deinococcus radiodurans	Mutation(s): 0
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 ID: 1
Molecule	Chains	Length	Organism	Image
23S ribosomal RNA	0	2880	Deinococcus radiodurans

Entity ID: 2
Molecule	Chains	Length	Organism	Image
tRNA acceptor stem mimic	5	35	N/A

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 = 169.9	α = 90
b = 409.9	β = 90
c = 695.9	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-02 
• 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