2Y95

Solution structure of AUCG tetraloop hairpin found in human Xist RNA A-repeats essential for X-inactivation


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: LEAST RESTRAINT VIOLATION, LOW ENERGY, AGREEMENT WITH CHEMICAL SHIFTS CALCULATED BY NUCHEMICS 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Xist RNA A-Repeat Comprises a Novel Aucg Tetraloop Fold and a Platform for Multimerization.

Duszczyk, M.M.Wutz, A.Rybin, V.Sattler, M.

(2011) RNA 17: 1973

  • DOI: https://doi.org/10.1261/rna.2747411
  • Primary Citation of Related Structures:  
    2Y95

  • PubMed Abstract: 

    X-chromosome inactivation (XCI) in female mammals depends on the noncoding RNA X inactivation specific transcript (Xist). The mechanism of chromosome-wide silencing by Xist is poorly understood. While it is established that the 5' region of Xist RNA, comprising the A-repeats and holding 7.5-8.5 copies of a conserved 26-mer sequence, is essential for Xist-mediated silencing, high-resolution structural information for the A-repeats is not available. Here, we report the three-dimensional solution structure of a 14-mer hairpin in the 5' region of a human A-repeat. This hairpin is remarkably stable and adopts a novel AUCG tetraloop fold, the integrity of which is required for silencing. We show that, contrary to previous predictions, the 3' region of single or tandem A-repeats mediates duplex formation in vitro. Significantly, mutations in this region disrupt the inter-repeat duplex formation in vitro and abrogate the silencing function of Xist A-repeats in vivo. Our data suggest that the complete A-repeat region may be stabilized by inter-repeat duplex formation and, as such, may provide a platform for multimerization and specific recognition of the AUCG tetraloops by trans-acting factors.


  • Organizational Affiliation

    Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-R(*GP*GP*CP*GP*CP*AP*UP*CP*GP*GP*CP*GP*CP*C)-3'14Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: LEAST RESTRAINT VIOLATION, LOW ENERGY, AGREEMENT WITH CHEMICAL SHIFTS CALCULATED BY NUCHEMICS 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2012-03-21
    Changes: Other
  • Version 1.2: 2018-01-24
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2023-06-14
    Changes: Data collection, Database references, Other