3G65 | pdb_00003g65

Crystal Structure of the Human Rad9-Rad1-Hus1 DNA Damage Checkpoint Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.272 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the rad9-rad1-hus1 DNA damage checkpoint complex--implications for clamp loading and regulation.

Dore, A.S.Kilkenny, M.L.Rzechorzek, N.J.Pearl, L.H.

(2009) Mol Cell 34: 735-745

  • DOI: https://doi.org/10.1016/j.molcel.2009.04.027
  • Primary Citation Related Structures: 
    3G65

  • PubMed Abstract: 

    Rad9, Rad1, and Hus1 form a heterotrimeric complex (9-1-1) that is loaded onto DNA at sites of DNA damage. DNA-loaded 9-1-1 activates signaling through the Chk1 arm of the DNA damage checkpoint response via recruitment and stimulation of ATR. Additionally, 9-1-1 may play a direct role in facilitating DNA damage repair via interaction with a number of DNA repair enzymes. We have now determined the crystal structure of the human 9-1-1 complex, revealing a toroidal structure with a similar architecture to the homotrimeric PCNA DNA-binding clamp. The structure explains the formation of a unique heterotrimeric arrangement and reveals significant differences among the three subunits in the sites implicated in binding to the clamp loader and to ligand proteins. Biochemical analysis reveals a single repair enzyme-binding site on 9-1-1 that can be blocked competitively by the PCNA-binding cell-cycle regulator p21(cip1/waf1).


  • Organizational Affiliation
    • CR-UK DNA Repair Enzymes Group, Section of Structural Biology, The Institute of Cancer Research, 237 Fulham Road, Chelsea, SW36JB London, UK.

Macromolecule Content 

  • Total Structure Weight: 96.04 kDa 
  • Atom Count: 6,150 
  • Modeled Residue Count: 773 
  • Deposited Residue Count: 858 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell cycle checkpoint control protein RAD9A296Homo sapiensMutation(s): 0 
Gene Names: RAD9RAD9A
EC: 3.1.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99638 (Homo sapiens)
Explore Q99638 
Go to UniProtKB:  Q99638
PHAROS:  Q99638
GTEx:  ENSG00000172613 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99638
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell cycle checkpoint protein RAD1282Homo sapiensMutation(s): 0 
Gene Names: RAD1REC1
EC: 3.1.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for O60671 (Homo sapiens)
Explore O60671 
Go to UniProtKB:  O60671
PHAROS:  O60671
GTEx:  ENSG00000113456 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60671
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Checkpoint protein HUS1280Homo sapiensMutation(s): 0 
Gene Names: HUS1
UniProt & NIH Common Fund Data Resources
Find proteins for O60921 (Homo sapiens)
Explore O60921 
Go to UniProtKB:  O60921
PHAROS:  O60921
GTEx:  ENSG00000136273 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60921
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.272 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.246α = 90
b = 70.673β = 99.51
c = 83.151γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-09-25
    Changes: Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Refinement description