Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.10 kDa 
• Atom Count: 470 
• Modelled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

1IE1

NMR Solution Structure of an In Vitro Selected RNA which is Sequence Specifically Recognized by Hamster Nucleolin RBD12.

• PDB DOI: 10.2210/pdb1IE1/pdb
• NDB: 1IE1

• Classification: RNA
• Mutation(s): No 


• Deposited: 2001-04-05 Released: 2001-06-20 
• Deposition Author(s): Bouvet, P., Allain, F.H.-T., Finger, L.D., Dieckmann, T., Feigon, J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 18 
• Conformers Submitted: 18 
• Selection Criteria: all calculated structures submitted 

Literature

Recognition of pre-formed and flexible elements of an RNA stem-loop by nucleolin.

Bouvet, P., Allain, F.H., Finger, L.D., Dieckmann, T., Feigon, J.

(2001) J Mol Biol 309: 763-775

• PubMed: 11397095 
• DOI: 10.1006/jmbi.2001.4691
• Primary Citation of Related Structures:  
  1IE1, 1IE2


• PubMed Abstract: 
  

Nucleolin is an abundant nucleolar protein which is essential for ribosome biogenesis. The first two of its four tandem RNA-binding domains (RBD12) specifically recognize a stem-loop structure containing a conserved UCCCGA sequence in the loop called the nucleolin-recognition element (NRE). We have determined the structure of the consensus SELEX NRE (sNRE) by NMR spectroscopy. In both the free and bound RNA the top part of the stem forms a loop E (or S-turn) motif. In the absence of protein, the structure of the hairpin loop is not well defined due to conformational heterogeneity, and appears to be in equilibrium between two families of conformations. Titrations of RBD1, RBD2, and RBD12 with the sNRE show that specific binding requires RBD12. In complex with RBD12, the hairpin loop interacts specifically with the protein and adopts a well-defined structure which shares some of the features of the free form. The loop E motif also has specific interactions with the protein. Implications of these findings for the mechanism of recognition of RNA structures by modular proteins are discussed.

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Organizational Affiliation: 

Laboratoire de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, Toulouse Cedex, 31077, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*CP*CP*GP*AP*AP*AP*UP*CP*CP*CP*GP*AP*AP*GP*UP*AP*GP*GP*CP*C)-3'	A	22	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 18 
• Conformers Submitted: 18 
• Selection Criteria: all calculated structures submitted 
• OLDERADO: 1IE1 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-04-05 
• Released Date: 2001-06-20 
Deposition Author(s): Bouvet, P., Allain, F.H.-T., Finger, L.D., Dieckmann, T., Feigon, J.

Revision History  

• Version 1.0: 2001-06-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-02-01
  Changes: Structure summary