Crystal structure of the DNA-binding protein DdrC from Deinococcus radiodurans

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.183 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction.

Banneville, A.S.Bouthier de la Tour, C.De Bonis, S.Hognon, C.Colletier, J.P.Teulon, J.M.Le Roy, A.Pellequer, J.L.Monari, A.Dehez, F.Confalonieri, F.Servant, P.Timmins, J.

(2022) Nucleic Acids Res 50: 7680-7696

  • DOI: https://doi.org/10.1093/nar/gkac563
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Deinococcus radiodurans is a spherical bacterium well-known for its outstanding resistance to DNA-damaging agents. Exposure to such agents leads to drastic changes in the transcriptome of D. radiodurans. In particular, four Deinococcus-specific genes, known as DNA Damage Response genes, are strongly up-regulated and have been shown to contribute to the resistance phenotype of D. radiodurans. One of these, DdrC, is expressed shortly after exposure to γ-radiation and is rapidly recruited to the nucleoid. In vitro, DdrC has been shown to compact circular DNA, circularize linear DNA, anneal complementary DNA strands and protect DNA from nucleases. To shed light on the possible functions of DdrC in D. radiodurans, we determined the crystal structure of the domain-swapped DdrC dimer at a resolution of 2.5 Å and further characterized its DNA binding and compaction properties. Notably, we show that DdrC bears two asymmetric DNA binding sites located on either side of the dimer and can modulate the topology and level of compaction of circular DNA. These findings suggest that DdrC may be a DNA damage-induced nucleoid-associated protein that enhances nucleoid compaction to limit the dispersion of the fragmented genome and facilitate DNA repair after exposure to severe DNA damaging conditions.

  • Organizational Affiliation

    Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage response protein C
A, B
235Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
Gene Names: ddrC
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.183 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.721α = 90
b = 111.721β = 90
c = 105.187γ = 120
Software Package:
Software NamePurpose
Cootmodel building
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
French Alternative Energies and Atomic Energy Commission (CEA)France--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-07-20
    Changes: Database references
  • Version 1.2: 2022-08-03
    Changes: Database references