1Z58

Crystal structure of a complex of the ribosome large subunit with rapamycin

• PDB DOI: https://doi.org/10.2210/pdb1Z58/pdb
• NAKB: 1Z58

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


• Deposited: 2005-03-17 Released: 2005-06-28 
• Deposition Author(s): Amit, M., Berisio, R., Baram, D., Harms, J., Bashan, A., Yonath, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.368 
• R-Value Work: 0.273 
• R-Value Observed: 0.304 

Literature

A crevice adjoining the ribosome tunnel: Hints for cotranslational folding.

Amit, M., Berisio, R., Baram, D., Harms, J., Bashan, A., Yonath, A.

(2005) FEBS Lett 579: 3207-3213

• PubMed: 15943964 
• DOI: https://doi.org/10.1016/j.febslet.2005.03.023
• Primary Citation of Related Structures:  
  1Z58


• PubMed Abstract: 
  

  RNA protection experiments and the crystal structure of a complex of the large ribosomal subunit from the eubacterium Deinococcus radiodurans with rapamycin, a polyketide compound resembling macrolides and ketolides, showed that rapamycin binds to a crevice located at the boundaries of the nascent protein exit tunnel, near its entrance. At this location rapamycin cannot occlude the ribosome exit tunnel, consistent with its failure to act as a ribosomal antibiotic drug. In accord with recent biochemical data, this crevice may play a role in facilitating local cotranslational folding of nascent chains, in particular for transmembrane proteins.

---

Organizational Affiliation: 

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

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 934.32 kDa 
• Atom Count: 59,424 
• 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 2]	2,880	Deinococcus radiodurans

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RAP	B [auth 2]	RAPAMYCIN IMMUNOSUPPRESSANT DRUG C51 H79 N O13 QFJCIRLUMZQUOT-HPLJOQBZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.368 
• R-Value Work: 0.273 
• R-Value Observed: 0.304 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.5	α = 90
b = 404	β = 90
c = 689	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-28 
Deposition Author(s): Amit, M., Berisio, R., Baram, D., Harms, J., Bashan, A., Yonath, A.

Revision History  

• Version 1.0: 2005-06-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations