4OL8 | pdb_00004ol8

Ty3 reverse transcriptase bound to DNA/RNA

• PDB DOI: https://doi.org/10.2210/pdb4OL8/pdb
• NAKB: 4OL8

• Classification: TRANSFERASE, HYDROLASE/RNA/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-01-23 Released: 2014-03-05 
• Deposition Author(s): Nowak, E., Miller, J.T., Bona, M.K., Studnicka, J., Szczepanowski, R.H., Jurkowski, J., Le Grice, S.F.J., Nowotny, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.296 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

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

• PubMed: 24608367 
• DOI: https://doi.org/10.1038/nsmb.2785
• Primary Citation Related Structures: 
  4OL8


• 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 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.

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Organizational Affiliation: 
• Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.
Reverse Transcriptase Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, Maryland, USA.
Biophysics Core Facility, International Institute of Molecular and Cell Biology, Warsaw, Poland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 241.73 kDa 
• Atom Count: 14,105 
• Modeled Residue Count: 1,715 
• Deposited Residue Count: 1,980 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H	A, B, G [auth F], H [auth E]	478	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: TY3B-G, YGRWTy3-1 POL, YGR109W-B, G5984 EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data)
UniProt
Find proteins for Q99315 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q99315  Go to UniProtKB:  Q99315

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*CP*UP*GP*AP*GP*AP*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*UP*G)-3'	C, E [auth G]	18	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*TP*CP*TP*TP*CP*CP*TP*CP*TP*CP*TP*CP*TP*C)-3'	D, F [auth H]	16	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, G [auth F], H [auth E]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.296 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 320.7	α = 90
b = 75.062	β = 90
c = 108.35	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
AutoSol	phasing
PHENIX	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-05 
Deposition Author(s): Nowak, E., Miller, J.T., Bona, M.K., Studnicka, J., Szczepanowski, R.H., Jurkowski, J., Le Grice, S.F.J., Nowotny, M.

Revision History  

• Version 1.0: 2014-03-05
  Type: Initial release
  
• Version 1.1: 2014-03-12
  Changes: Structure summary
• Version 1.2: 2014-04-02
  Changes: Database references
• Version 1.3: 2014-04-16
  Changes: Database references
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary