Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 986338.38 
• Atom Count: 60249 
• Residue Count: 3293 
• 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, Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)


• 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: 3.5 Å
• R-Value Free: 0.295 
• R-Value Work: 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 
• Primary Citation of Related Structures:  
  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

Find similar proteins by: Sequence  |  Structure

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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
GENERAL STRESS PROTEIN CTC	T	237	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)	Mutation(s): 0  Gene Names: rplY (ctc)
Find proteins for Q9RX88 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Go to UniProtKB:  Q9RX88

Entity ID: 1
Molecule	Chains	Length	Organism
23S ribosomal RNA	0	2880	Deinococcus radiodurans

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PPU	5	RNA LINKING	C22 H30 N7 O8 P		A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.5 Å
• R-Value Free: 0.295 
• R-Value Work: 0.244 
• Space Group: I 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 169.900	α = 90.00
b = 409.900	β = 90.00
c = 695.900	γ = 90.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance