3KYL | pdb_00003kyl

Structure of the catalytic subunit of telomerase bound to its RNA template and telomeric DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.287 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3KYL

This is version 1.5 of the entry. See complete history

Literature

Structural basis for telomerase catalytic subunit TERT binding to RNA template and telomeric DNA.

Mitchell, M.Gillis, A.Futahashi, M.Fujiwara, H.Skordalakes, E.

(2010) Nat Struct Mol Biol 17: 513-518

  • DOI: https://doi.org/10.1038/nsmb.1777
  • Primary Citation Related Structures: 
    3KYL

  • PubMed Abstract: 

    Telomerase is a specialized DNA polymerase that extends the 3' ends of eukaryotic linear chromosomes, a process required for genomic stability and cell viability. Here we present the crystal structure of the active Tribolium castaneum telomerase catalytic subunit, TERT, bound to an RNA-DNA hairpin designed to resemble the putative RNA-templating region and telomeric DNA. The RNA-DNA hybrid adopts a helical structure, docked in the interior cavity of the TERT ring. Contacts between the RNA template and motifs 2 and B' position the solvent-accessible RNA bases close to the enzyme active site for nucleotide binding and selectivity. Nucleic acid binding induces rigid TERT conformational changes to form a tight catalytic complex. Overall, TERT-RNA template and TERT-telomeric DNA associations are remarkably similar to those observed for retroviral reverse transcriptases, suggesting common mechanistic aspects of DNA replication between the two families of enzymes.


  • Organizational Affiliation
    • Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania, USA.

Macromolecule Content 

  • Total Structure Weight: 78.11 kDa 
  • Atom Count: 5,535 
  • Modeled Residue Count: 620 
  • Deposited Residue Count: 620 
  • Unique protein chains: 1
  • Unique hybrid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Telomerase reverse transcriptase596Tribolium castaneumMutation(s): 0 
Gene Names: TERT
EC: 2.7.7.49
UniProt
Find proteins for Q0QHL8 (Tribolium castaneum)
Explore Q0QHL8 
Go to UniProtKB:  Q0QHL8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0QHL8
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA/RNA (5'-R(*CP*UP*GP*AP*CP*CP*UP*GP*AP*C)-D(P*TP*TP*CP*GP*GP*TP*CP*AP*GP*GP*TP*CP*AP*G)-3')B [auth E]24N/A
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.287 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.231α = 90
b = 52.782β = 101.9
c = 101.609γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
ELVESrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-02-22
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-02-21
    Changes: Data collection, Database references, Derived calculations