5KQE

Solution structure of P2a-J2a/b-P2b of medaka telomerase RNA

  • Classification: RNA
  • Organism(s): Oryzias latipes
  • Mutation(s): No 

  • Deposited: 2016-07-06 Released: 2016-08-24 
  • Deposition Author(s): Wang, Y., Feigon, J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human.

Wang, Y.Yesselman, J.D.Zhang, Q.Kang, M.Feigon, J.

(2016) Proc Natl Acad Sci U S A 113: E5125-E5134

  • DOI: https://doi.org/10.1073/pnas.1607411113
  • Primary Citation of Related Structures:  
    5KQE

  • PubMed Abstract: 

    Telomerase is an RNA-protein complex that includes a unique reverse transcriptase that catalyzes the addition of single-stranded telomere DNA repeats onto the 3' ends of linear chromosomes using an integral telomerase RNA (TR) template. Vertebrate TR contains the template/pseudoknot (t/PK) and CR4/5 domains required for telomerase activity in vitro. All vertebrate pseudoknots include two subdomains: P2ab (helices P2a and P2b with a 5/6-nt internal loop) and the minimal pseudoknot (P2b-P3 and associated loops). A helical extension of P2a, P2a.1, is specific to mammalian TR. Using NMR, we investigated the structures of the full-length TR pseudoknot and isolated subdomains in Oryzias latipes (Japanese medaka fish), which has the smallest vertebrate TR identified to date. We determined the solution NMR structure and studied the dynamics of medaka P2ab, and identified all base pairs and tertiary interactions in the minimal pseudoknot. Despite differences in length and sequence, the structure of medaka P2ab is more similar to human P2ab than predicted, and the medaka minimal pseudoknot has the same tertiary interactions as the human pseudoknot. Significantly, although P2a.1 is not predicted to form in teleost fish, we find that it forms in the full-length pseudoknot via an unexpected hairpin. Model structures of the subdomains are combined to generate a model of t/PK. These results provide evidence that the architecture for the vertebrate t/PK is conserved from teleost fish to human. The organization of the t/PK on telomerase reverse transcriptase for medaka and human is modeled based on the cryoEM structure of Tetrahymena telomerase, providing insight into function.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569;


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Telomerase RNA P2ab36Oryzias latipes
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM48123
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM112503
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM112294
National Science Foundation (NSF, United States)United StatesMCB1517625
Department of Energy (DOE, United States)United StatesDE-FC03-02ER63421

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-08-31
    Changes: Database references
  • Version 1.2: 2016-09-14
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Database references, Structure summary
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence, Data collection
  • Version 1.5: 2023-06-14
    Changes: Database references, Other
  • Version 1.6: 2024-05-15
    Changes: Data collection, Database references