2H1M

Synthesis, Oxidation Behavior, Crystallization and Structure of 2'-Methylseleno Guanosine Containing RNAs

  • Classification: RNA
  • Mutation(s): No 

  • Deposited: 2006-05-16 Released: 2006-07-18 
  • Deposition Author(s): Serganov, A.A.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Synthesis, Oxidation Behavior, Crystallization and Structure of 2'-Methylseleno Guanosine Containing RNAs.

Moroder, H.Kreutz, C.Lang, K.Serganov, A.Micura, R.

(2006) J Am Chem Soc 128: 9909-9918

  • DOI: 10.1021/ja0621400
  • Primary Citation of Related Structures:  
    2H1M

  • PubMed Abstract: 
  • We have recently introduced a basic concept for the combined chemical and enzymatic preparation of site-specifically modified 2'-methylseleno RNAs which represent useful derivatives for phasing of X-ray crystallographic data during their three-dimensional structure determination ...

    We have recently introduced a basic concept for the combined chemical and enzymatic preparation of site-specifically modified 2'-methylseleno RNAs which represent useful derivatives for phasing of X-ray crystallographic data during their three-dimensional structure determination. Here, we introduce the first synthesis of an appropriate guanosine phosphoramidite, which complements the thus far established set of 2'-methylseleno-modified uridine, cytidine, and adenosine building blocks for solid-phase synthesis. The novel building block was readily incorporated into RNA. Importantly, it was the 2'-methylseleno-guanosine-labeled RNA that allowed us to reveal the reversible oxidation/reduction behavior of the Se moiety and thus it represents a valuable contribution to the understanding of the action of threo-1,4-dimercapto-2,3-butanediol (DTT) required during solid-phase synthesis, deprotection, and crystallization of selenium-containing RNA. In addition, we investigated 2'-methylseleno RNA with respect to crystallization properties. Our studies revealed that the Se modification significantly increases the range of conditions leading to crystal growth. Moreover, we determined the crystal structures of model RNA helices and showed that the Se modification can affect crystal packing interactions, thus potentially expanding the possibilities for obtaining the best crystal form.


    Related Citations: 
    • Syntheses of RNAs with up to 100 nucleotides containing site-specific 2'-methylseleno labels for use in X-ray crystallography.
      Hobartner, C., Rieder, R., Kreutz, C., Puffer, B., Lang, K., Polonskaia, A., Serganov, A.A., Micura, R.
      (2005) J Am Chem Soc 127: 12035
    • Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation.
      Serganov, A.A., Keiper, S., Malinina, L., Tereshko, V., Skripkin, E., Hobartner, C., Polonskaia, A., Phan, A.T., Wombacher, R., Micura, R., Dauter, Z., Jaschke, A., Patel, D.J.
      (2005) Nat Struct Mol Biol 12: 218

    Organizational Affiliation

    Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria.



Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*GP*CP*AP*(XUG)P*AP*GP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'A, B 16N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.314α = 90
b = 46.314β = 90
c = 128.348γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CBASSdata collection
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2006-05-16 
  • Released Date: 2006-07-18 
  • Deposition Author(s): Serganov, A.A.

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance