Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.30 kDa 
• Atom Count: 1906 
• Modelled Residue Count: 86 
• Deposited Residue Count: 86 
• Unique nucleic acid chains: 1

2I7Z

GAAA tetraloop receptor complex with associated manganese ions.

• PDB DOI: 10.2210/pdb2I7Z/pdb
• NDB: 2I7Z

• Classification: RIBONUCLEIC ACID
• Mutation(s): No 


• Deposited: 2006-08-31 Released: 2007-04-03 
• Deposition Author(s): Davis, J.H., Butcher, S.E.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Role of metal ions in the tetraloop-receptor complex as analyzed by NMR.

Davis, J.H., Foster, T.R., Tonelli, M., Butcher, S.E.

(2007) RNA 13: 76-86

• PubMed: 17119098 
• DOI: 10.1261/rna.268307
• Primary Citation of Related Structures:  
  2I7E, 2I7Z


• PubMed Abstract: 
  

Metal ions are critical for the proper folding of RNA, and the GAAA tetraloop-receptor is necessary for the optimal folding and function of many RNAs. We have used NMR to investigate the role of metal ions in the structure of the tetraloop-receptor in solution. The NMR data indicate native tertiary structure is formed under a wide range of ionic conditions. The lack of conformational adaptation in response to very different ionic conditions argues against a structural role for divalent ions. Nuclear Overhauser effects to cobalt hexammine and paramagnetic relaxation enhancement induced by manganese ions were used to determine the NMR structures of the tetraloop receptor in association with metal ions, providing the first atomic-level view of these interactions in the solution state. Five manganese and two cobalt hexammine ions could be localized to the RNA surface. The locations of the associated metal ions are similar, but not identical to, those of previously determined crystal structures. The sites of association are in general agreement with nonlinear Poisson-Boltzmann calculations of the electrostatic surface, emphasizing the general importance of diffusely associated ions in RNA tertiary structure.

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Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
43-MER	A, B	43	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2I7Z Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-08-31 
• Released Date: 2007-04-03 
Deposition Author(s): Davis, J.H., Butcher, S.E.

Revision History  

• Version 1.0: 2007-04-03
  Type: Initial release
  
• Version 1.1: 2007-10-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-12-28
  Changes: Advisory