1Q29 | pdb_00001q29

Hammerhead Ribozyme with 5'-5' G-G linkage: Conformational change experiment

• PDB DOI: https://doi.org/10.2210/pdb1Q29/pdb
• NAKB: 1Q29

• Classification: RNA
• Mutation(s): No 


• Deposited: 2003-07-23 Released: 2004-02-24 
• Deposition Author(s): Dunham, C.M., Murray, J.B., Scott, W.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.279 (Depositor) 
• R-Value Work: 
  0.242 (Depositor) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

A helical twist-induced conformational switch activates cleavage in the hammerhead ribozyme.

Dunham, C.M., Murray, J.B., Scott, W.G.

(2003) J Mol Biology 332: 327-336

• PubMed: 12948485 
• DOI: https://doi.org/10.1016/s0022-2836(03)00843-x
• Primary Citation Related Structures: 
  1NYI, 1Q29


• PubMed Abstract: 
  

  We have captured the structure of a pre-catalytic conformational intermediate of the hammerhead ribozyme using a phosphodiester tether formed between I and Stem II. This phosphodiester tether appears to mimic interactions in the wild-type hammerhead RNA that enable switching between nuclease and ligase activities, both of which are required in the replicative cycles of the satellite RNA viruses from which the hammerhead ribozyme is derived. The structure of this conformational intermediate reveals how the attacking nucleophile is positioned prior to cleavage, and demonstrates how restricting the ability of Stem I to rotate about its helical axis, via interactions with Stem II, can inhibit cleavage. Analogous covalent crosslinking experiments have demonstrated that imposing such restrictions on interhelical movement can change the hammerhead ribozyme from a nuclease to a ligase. Taken together, these results permit us to suggest that switching between ligase and nuclease activity is determined by the helical orientation of Stem I relative to Stem II.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.48 kDa 
• Atom Count: 877 
• Modeled Residue Count: 41 
• Deposited Residue Count: 41 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3'	A	17	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Ribozyme	B	24	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.279 (Depositor) 
• R-Value Work:  0.242 (Depositor) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.689	α = 90
b = 66.689	β = 90
c = 140.528	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-24 
Deposition Author(s): Dunham, C.M., Murray, J.B., Scott, W.G.

Revision History  

• Version 1.0: 2004-02-24
  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: 2019-07-24
  Changes: Advisory, Data collection, Derived calculations, Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description