ATP-dependent DNA ligase from S. solfataricus

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


A Flexible Interface between DNA Ligase and PCNA Supports Conformational Switching and Efficient Ligation of DNA.

Pascal, J.M.Tsodikov, O.V.Hura, G.L.Song, W.Cotner, E.A.Classen, S.Tomkinson, A.E.Tainer, J.A.Ellenberger, T.

(2006) Mol Cell 24: 279-291

  • DOI: https://doi.org/10.1016/j.molcel.2006.08.015
  • Primary Citation of Related Structures:  
    2HII, 2HIK, 2HIV, 2HIX

  • PubMed Abstract: 

    DNA sliding clamps encircle DNA and provide binding sites for many DNA-processing enzymes. However, it is largely unknown how sliding clamps like proliferating cell nuclear antigen (PCNA) coordinate multistep DNA transactions. We have determined structures of Sulfolobus solfataricus DNA ligase and heterotrimeric PCNA separately by X-ray diffraction and in complex by small-angle X-ray scattering (SAXS). Three distinct PCNA subunits assemble into a protein ring resembling the homotrimeric PCNA of humans but with three unique protein-binding sites. In the absence of nicked DNA, the Sulfolobus solfataricus DNA ligase has an open, extended conformation. When complexed with heterotrimeric PCNA, the DNA ligase binds to the PCNA3 subunit and ligase retains an open, extended conformation. A closed, ring-shaped conformation of ligase catalyzes a DNA end-joining reaction that is strongly stimulated by PCNA. This open-to-closed switch in the conformation of DNA ligase is accommodated by a malleable interface with PCNA that serves as an efficient platform for DNA ligation.

  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thermostable DNA ligase621Saccharolobus solfataricusMutation(s): 0 
Gene Names: lig
Find proteins for Q980T8 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q980T8 
Go to UniProtKB:  Q980T8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ980T8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.206α = 90
b = 169.77β = 90
c = 77.31γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description