4CHT

Crystal structure of the human topoisomerase III alpha-RMI1 complex with bound calcium ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Mechanistic Insight Into Holliday-Junction Dissolution by Topoisomerase Iiialpha and Rmi1

Bocquet, N.Bizard, A.H.Abdulrahman, W.Larsen, N.B.Faty, M.Cavadini, S.Bunker, R.D.Kowalczykowski, S.C.Cejka, P.Hickson, I.D.Thoma, N.H.

(2014) Nat.Struct.Mol.Biol. 21: 261

  • DOI: 10.1038/nsmb.2775
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Repair of DNA double-strand breaks via homologous recombination can produce double Holliday junctions (dHJs) that require enzymatic separation. Topoisomerase IIIα (TopIIIα) together with RMI1 disentangles the final hemicatenane intermediate obtained ...

    Repair of DNA double-strand breaks via homologous recombination can produce double Holliday junctions (dHJs) that require enzymatic separation. Topoisomerase IIIα (TopIIIα) together with RMI1 disentangles the final hemicatenane intermediate obtained once dHJs have converged. How binding of RMI1 to TopIIIα influences it to behave as a hemicatenane dissolvase, rather than as an enzyme that relaxes DNA topology, is unknown. Here, we present the crystal structure of human TopIIIα complexed to the first oligonucleotide-binding domain (OB fold) of RMI1. TopIII assumes a toroidal type 1A topoisomerase fold. RMI1 attaches to the edge of the gate in TopIIIα through which DNA passes. RMI1 projects a 23-residue loop into the TopIIIα gate, thereby influencing the dynamics of its opening and closing. Our results provide a mechanistic rationale for how RMI1 stabilizes TopIIIα-gate opening to enable dissolution and illustrate how binding partners modulate topoisomerase function.


    Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA TOPOISOMERASE 3-ALPHA
A
755Homo sapiensMutation(s): 0 
Gene Names: TOP3A (TOP3)
EC: 5.99.1.2
Find proteins for Q13472 (Homo sapiens)
Go to Gene View: TOP3A
Go to UniProtKB:  Q13472
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1
B
219Homo sapiensMutation(s): 0 
Gene Names: RMI1 (C9orf76)
Find proteins for Q9H9A7 (Homo sapiens)
Go to Gene View: RMI1
Go to UniProtKB:  Q9H9A7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.360α = 90.00
b = 93.360β = 90.00
c = 381.620γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Database references
  • Version 1.2: 2014-03-19
    Type: Database references