6IY5

NMR solution structures of 5'-ATTCTATTCT-3


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Minidumbbell structures formed by ATTCT pentanucleotide repeats in spinocerebellar ataxia type 10.

Guo, P.Lam, S.L.

(2020) Nucleic Acids Res 

  • DOI: 10.1093/nar/gkaa495
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Spinocerebellar ataxia type 10 (SCA10) is a progressive genetic disorder caused by ATTCT pentanucleotide repeat expansions in intron 9 of the ATXN10 gene. ATTCT repeats have been reported to form unwound secondary structures which are likely linked t ...

    Spinocerebellar ataxia type 10 (SCA10) is a progressive genetic disorder caused by ATTCT pentanucleotide repeat expansions in intron 9 of the ATXN10 gene. ATTCT repeats have been reported to form unwound secondary structures which are likely linked to large-scale repeat expansions. In this study, we performed high-resolution nuclear magnetic resonance spectroscopic investigations on DNA sequences containing two to five ATTCT repeats. Strikingly, we found the first two repeats of all these sequences well folded into highly compact minidumbbell (MDB) structures. The 3D solution structure of the sequence containing two ATTCT repeats was successfully determined, revealing the MDB comprises a regular TTCTA and a quasi TTCT/A pentaloops with extensive stabilizing loop-loop interactions. We further carried out in vitro primer extension assays to examine if the MDB formed in the primer could escape from the proofreading function of DNA polymerase. Results showed that when the MDB was formed at 5-bp or farther away from the priming site, it was able to escape from the proofreading by Klenow fragment of DNA polymerase I and thus retained in the primer. The intriguing structural findings bring about new insights into the origin of genetic instability in SCA10.


    Organizational Affiliation

    Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*TP*CP*TP*AP*TP*TP*CP*T)-3')A10Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 6IY5 Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-12-13 
  • Released Date: 2020-06-10 
  • Deposition Author(s): Lam, S.L., Guo, P.

Revision History 

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-06-24
    Changes: Database references