359D | pdb_0000359d

INHIBITION OF THE HAMMERHEAD RIBOZYME CLEAVAGE REACTION BY SITE-SPECIFIC BINDING OF TB(III)

• PDB DOI: https://doi.org/10.2210/pdb359D/pdb
• NAKB: 359D

• Classification: RIBOZYME
• Mutation(s): No 


• Deposited: 1997-10-27 Released: 1997-11-07 
• Deposition Author(s): Feig, A.L., Scott, W.G., Uhlenbeck, O.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.302 (Depositor) 
• R-Value Work: 
  0.256 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Starting Model: experimental

Literature

Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb.

Feig, A.L., Scott, W.G., Uhlenbeck, O.C.

(1998) Science 279: 81-84

• PubMed: 9417029 
• DOI: https://doi.org/10.1126/science.279.5347.81
• Primary Citation Related Structures: 
  359D


• PubMed Abstract: 
  

  Terbium(III) [Tb(III)] was shown to inhibit the hammerhead ribozyme by competing with a single magnesium(II) ion. X-ray crystallography revealed that the Tb(III) ion binds to a site adjacent to an essential guanosine in the catalytic core of the ribozyme, approximately 10 angstroms from the cleavage site. Synthetic modifications near this binding site yielded an RNA substrate that was resistant to Tb(III) binding and capable of being cleaved, even in the presence of up to 20 micromolar Tb(III). It is suggested that the magnesium(II) ion thought to bind at this site may act as a switch, affecting the conformational changes required to achieve the transition state.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.98 kDa 
• Atom Count: 878 
• Modeled Residue Count: 41 
• Deposited Residue Count: 41 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA HAMMERHEAD RIBOZYME	A	16	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA HAMMERHEAD RIBOZYME	B	25	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TB	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.302 (Depositor) 
• R-Value Work:  0.256 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.54	α = 90
b = 65.54	β = 90
c = 138.08	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-11-07 
Deposition Author(s): Feig, A.L., Scott, W.G., Uhlenbeck, O.C.

Revision History  

• Version 1.0: 1997-11-07
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description