4OL8

Ty3 reverse transcriptase bound to DNA/RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry.

Nowak, E.Miller, J.T.Bona, M.K.Studnicka, J.Szczepanowski, R.H.Jurkowski, J.Le Grice, S.F.Nowotny, M.

(2014) Nat.Struct.Mol.Biol. 21: 389-396

  • DOI: 10.1038/nsmb.2785

  • PubMed Abstract: 
  • Retrotransposons are a class of mobile genetic elements that replicate by converting their single-stranded RNA intermediate to double-stranded DNA through the combined DNA polymerase and ribonuclease H (RNase H) activities of the element-encoded reve ...

    Retrotransposons are a class of mobile genetic elements that replicate by converting their single-stranded RNA intermediate to double-stranded DNA through the combined DNA polymerase and ribonuclease H (RNase H) activities of the element-encoded reverse transcriptase (RT). Although a wealth of structural information is available for lentiviral and gammaretroviral RTs, equivalent studies on counterpart enzymes of long terminal repeat (LTR)-containing retrotransposons, from which they are evolutionarily derived, is lacking. In this study, we report the first crystal structure of a complex of RT from the Saccharomyces cerevisiae LTR retrotransposon Ty3 in the presence of its polypurine tract-containing RNA-DNA hybrid. In contrast to its retroviral counterparts, Ty3 RT adopts an asymmetric homodimeric architecture whose assembly is substrate dependent. Moreover, our structure and biochemical data suggest that the RNase H and DNA polymerase activities are contributed by individual subunits of the homodimer.


    Organizational Affiliation

    Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase/ribonuclease H
A, B, F, E
478Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: TY3B-G (YGRWTy3-1 POL)
EC: 3.1.26.4, 2.7.7.49, 2.7.7.7, 3.4.23.-
Find proteins for Q99315 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q99315
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*CP*UP*GP*AP*GP*AP*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*UP*G)-3'C,G18N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*AP*TP*CP*TP*TP*CP*CP*TP*CP*TP*CP*TP*CP*TP*C)-3'D,H16N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 320.700α = 90.00
b = 75.062β = 90.00
c = 108.350γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
AutoSolphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Structure summary
  • Version 1.2: 2014-04-02
    Type: Database references
  • Version 1.3: 2014-04-16
    Type: Database references