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 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    4CHT, 4CGY

  • 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 once ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA TOPOISOMERASE 3-ALPHA A755Homo sapiensMutation(s): 0 
Gene Names: TOP3ATOP3
EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
Find proteins for Q13472 (Homo sapiens)
Explore Q13472 
Go to UniProtKB:  Q13472
NIH Common Fund Data Resources
PHAROS:  Q13472
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1 B219Homo sapiensMutation(s): 0 
Gene Names: RMI1C9orf76
Find proteins for Q9H9A7 (Homo sapiens)
Explore Q9H9A7 
Go to UniProtKB:  Q9H9A7
NIH Common Fund Data Resources
PHAROS:  Q9H9A7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates 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 
  • R-Value Observed: 0.198 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.36α = 90
b = 93.36β = 90
c = 381.62γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references
  • Version 1.2: 2014-03-19
    Changes: Database references
  • Version 1.3: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy