6BY5 | pdb_00006by5

Two-State 14-mer UUCG Tetraloop calculated from Exact NOEs (State one: Conformers 1-5, State Two: Conformers 6-10)

• PDB DOI: https://doi.org/10.2210/pdb6BY5/pdb
• NAKB: 6BY5
• BMRB: 30386

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2017-12-19 Released: 2018-06-13 
• Deposition Author(s): Nichols, P.J., Henen, M.A., Born, A., Strotz, D., Guntert, P., Vogeli, B.
• Funding Organization(s): University of Colorado Anschutz Medical Campus

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: target function 

Literature

High-resolution small RNA structures from exact nuclear Overhauser enhancement measurements without additional restraints.

Nichols, P.J., Henen, M.A., Born, A., Strotz, D., Guntert, P., Vogeli, B.

(2018) Commun Biol 1: 61-61

• PubMed: 30271943 
• DOI: https://doi.org/10.1038/s42003-018-0067-x
• Primary Citation Related Structures: 
  6BY4, 6BY5


• PubMed Abstract: 
  

  RNA not only translates the genetic code into proteins, but also carries out important cellular functions. Understanding such functions requires knowledge of the structure and dynamics at atomic resolution. Almost half of the published RNA structures have been solved by nuclear magnetic resonance (NMR). However, as a result of severe resonance overlap and low proton density, high-resolution RNA structures are rarely obtained from nuclear Overhauser enhancement (NOE) data alone. Instead, additional semi-empirical restraints and labor-intensive techniques are required for structural averages, while there are only a few experimentally derived ensembles representing dynamics. Here we show that our exact NOE (eNOE) based structure determination protocol is able to define a 14-mer UUCG tetraloop structure at high resolution without other restraints. Additionally, we use eNOEs to calculate a two-state structure, which samples its conformational space. The protocol may open an avenue to obtain high-resolution structures of small RNA of unprecedented accuracy with moderate experimental efforts.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora,, CO, 80045, USA.
Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
Laboratory of Physical Chemistry, ETH Zürich, ETH-Hönggerberg, Zürich, 8093, Switzerland.
Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, 60438, Germany.
Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, 192-0397, Japan.
Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora,, CO, 80045, USA. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.45 kDa 
• Atom Count: 297 
• Modeled Residue Count: 14 
• Deposited Residue Count: 14 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*GP*CP*AP*CP*UP*UP*CP*GP*GP*UP*GP*CP*C)-3')	A	14	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: target function 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Nichols, P.J., Henen, M.A., Born, A., Strotz, D., Guntert, P., Vogeli, B.

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Funding Organization	Location	Grant Number
University of Colorado Anschutz Medical Campus	United States	--

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release
  
• Version 1.1: 2018-10-17
  Changes: Data collection, Database references
• Version 1.2: 2023-06-14
  Changes: Database references, Other
• Version 1.3: 2024-05-22
  Changes: Data collection