4CGY | pdb_00004cgy

Crystal structure of the human topoisomerase III alpha-RMI1 complex

• PDB DOI: https://doi.org/10.2210/pdb4CGY/pdb

• Classification: DNA REPLICATION/ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2013-11-27 Released: 2014-02-12 
• Deposition Author(s): Bocquet, N., Bunker, R.D., Thoma, N.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.231 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Models: experimental

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

• PubMed: 24509834 
• DOI: https://doi.org/10.1038/nsmb.2775
• Primary Citation Related Structures: 
  4CGY, 4CHT


• 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 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.

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Organizational Affiliation: 
• Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA.
1] Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA. [2].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 111.25 kDa 
• Atom Count: 6,602 
• Modeled Residue Count: 824 
• Deposited Residue Count: 973 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA TOPOISOMERASE 3-ALPHA	A	754	Homo sapiens	Mutation(s): 0  EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13472 (Homo sapiens) Explore Q13472  Go to UniProtKB:  Q13472
PHAROS:  Q13472 GTEx:  ENSG00000177302

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1	B	219	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9A7 (Homo sapiens) Explore Q9H9A7  Go to UniProtKB:  Q9H9A7
PHAROS:  Q9H9A7 GTEx:  ENSG00000178966

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.231 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.01	α = 90
b = 94.01	β = 90
c = 381.69	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Bocquet, N., Bunker, R.D., Thoma, N.H.

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
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description