5GVD

Human TDRD3 DUF1767-OB domains

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.623 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Structural basis of the interaction between Topoisomerase III beta and the TDRD3 auxiliary factor

Goto-Ito, S., Yamagata, A., Takahashi, T.S., Sato, Y., Fukai, S.

(2017) Sci Rep 7: 42123-42123

  • DOI: 10.1038/srep42123
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Topoisomerase IIIβ (TOP3β) is a DNA/RNA topoisomerase that has been implicated in epigenetic or translational control of gene expression. In cells, TOP3β co-exists with its specific auxiliary factor, TDRD3. TDRD3 serves as a scaffold protein to recru ...

    Topoisomerase IIIβ (TOP3β) is a DNA/RNA topoisomerase that has been implicated in epigenetic or translational control of gene expression. In cells, TOP3β co-exists with its specific auxiliary factor, TDRD3. TDRD3 serves as a scaffold protein to recruit TOP3β to its DNA/RNA substrates accumulating in specific cellular sites such as methylated chromatins or neural stress granules. Here we report the crystal structures of the catalytic domain of TOP3β, the DUF1767-OB-fold domains of TDRD3 and their complex at 3.44 Å, 1.62 Å and 3.6 Å resolutions, respectively. The toroidal-shaped catalytic domain of TOP3β binds the OB-fold domain of TDRD3. The TDRD3 OB-fold domain harbors the insertion loop, which is protruding from the core structure. Both the insertion loop and core region interact with TOP3β. Our pull-down binding assays showed that hydrophobic characters of the core surface and the amino- and carboxy-terminal regions of the insertion loop are essential for the interaction. Furthermore, by comparison with the structure of the homologous Topoisomerase IIIα (TOP3α)-RMI1 complex, we identified Arg96, Val109, Phe139 and the short insertion loop of TDRD3 as the critical structural elements for the specific interaction with TOP3β to avoid the non-cognate interaction with TOP3α.

    Organizational Affiliation: 

    Structural Biology Laboratory, Structural Life Science Division, Synchrotron Radiation Research Organization and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tudor domain-containing protein 3
A, B
165Homo sapiensMutation(s): 0 
Gene Names: TDRD3
Find proteins for Q9H7E2 (Homo sapiens)
Go to Gene View: TDRD3
Go to UniProtKB:  Q9H7E2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.623 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.175 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 85.669α = 90.00
b = 85.669β = 90.00
c = 104.207γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
DENZOdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release