Crystal structure of the K. lactis Rad5

Experimental Data Snapshot

  • Resolution: 3.60 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

Starting Model: experimental
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Structural basis for the multi-activity factor Rad5 in replication stress tolerance.

Shen, M.Dhingra, N.Wang, Q.Cheng, C.Zhu, S.Tian, X.Yu, J.Gong, X.Li, X.Zhang, H.Xu, X.Zhai, L.Xie, M.Gao, Y.Deng, H.He, Y.Niu, H.Zhao, X.Xiang, S.

(2021) Nat Commun 12: 321-321

  • DOI: https://doi.org/10.1038/s41467-020-20538-w
  • Primary Citation of Related Structures:  
    6L8N, 6L8O

  • PubMed Abstract: 

    The yeast protein Rad5 and its orthologs in other eukaryotes promote replication stress tolerance and cell survival using their multiple activities, including ubiquitin ligase, replication fork remodeling and DNA lesion targeting activities. Here, we present the crystal structure of a nearly full-length Rad5 protein. The structure shows three distinct, but well-connected, domains required for Rad5's activities. The spatial arrangement of these domains suggest that different domains can have autonomous activities but also undergo intrinsic coordination. Moreover, our structural, biochemical and cellular studies demonstrate that Rad5's HIRAN domain mediates interactions with the DNA metabolism maestro factor PCNA and contributes to its poly-ubiquitination, binds to DNA and contributes to the Rad5-catalyzed replication fork regression, defining a new type of HIRAN domains with multiple activities. Our work provides a framework to understand how Rad5 integrates its various activities in replication stress tolerance.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, P. R. China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein RAD5952Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: RAD5KLLA0F17479g
EC: 3.6.4
Find proteins for Q6CJM4 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q6CJM4 
Go to UniProtKB:  Q6CJM4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CJM4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.60 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.539α = 90
b = 188.539β = 90
c = 198.231γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31870769

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2021-01-27
    Changes: Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references
  • Version 1.4: 2024-04-03
    Changes: Refinement description