8WU8

Crystal structure of the human RAD9-RAD1(F64A/M256A/F266A)-HUS1-RHINO(88-99) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.220 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for intra- and intermolecular interactions on RAD9 subunit of 9-1-1 checkpoint clamp implies functional 9-1-1 regulation by RHINO.

Hara, K.Tatsukawa, K.Nagata, K.Iida, N.Hishiki, A.Ohashi, E.Hashimoto, H.

(2024) J Biol Chem 300: 105751-105751

  • DOI: https://doi.org/10.1016/j.jbc.2024.105751
  • Primary Citation of Related Structures:  
    8WU8

  • PubMed Abstract: 

    Eukaryotic DNA clamp is a trimeric protein featuring a toroidal ring structure that binds DNA on the inside of the ring and multiple proteins involved in DNA transactions on the outside. Eukaryotes have two types of DNA clamps: the replication clamp PCNA and the checkpoint clamp RAD9-RAD1-HUS1 (9-1-1). 9-1-1 activates the ATR-CHK1 pathway in DNA damage checkpoint, regulating cell cycle progression. Structure of 9-1-1 consists of two moieties: a hetero-trimeric ring formed by PCNA-like domains of three subunits and an intrinsically disordered C-terminal region of the RAD9 subunit, called RAD9 C-tail. The RAD9 C-tail interacts with the 9-1-1 ring and disrupts the interaction between 9-1-1 and DNA, suggesting a negative regulatory role for this intramolecular interaction. In contrast, RHINO, a 9-1-1 binding protein, interacts with both RAD1 and RAD9 subunits, positively regulating checkpoint activation by 9-1-1. This study presents a biochemical and structural analysis of intra- and inter-molecular interactions on the 9-1-1 ring. Biochemical analysis indicates that RAD9 C-tail binds to the hydrophobic pocket on the PCNA-like domain of RAD9, implying that the pocket is involved in multiple protein-protein interactions. The crystal structure of the 9-1-1 ring in complex with a RHINO peptide reveals that RHINO binds to the hydrophobic pocket of RAD9, shedding light on the RAD9-binding motif. Additionally, the study proposes a structural model of the 9-1-1-RHINO quaternary complex. Together, these findings provide functional insights into the intra- and inter-molecular interactions on the front side of RAD9, elucidating the roles of RAD9 C-tail and RHINO in checkpoint activation.


  • Organizational Affiliation

    School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell cycle checkpoint control protein RAD9A270Homo sapiensMutation(s): 0 
Gene Names: RAD9A
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Checkpoint protein HUS1286Homo 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cell cycle checkpoint protein RAD1282Homo sapiensMutation(s): 3 
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
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RAD9, HUS1, RAD1-interacting nuclear orphan protein 112Homo sapiensMutation(s): 0 
Gene Names: RHNO1C12orf32RHINOHKMT1188
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BSD3 (Homo sapiens)
Explore Q9BSD3 
Go to UniProtKB:  Q9BSD3
PHAROS:  Q9BSD3
GTEx:  ENSG00000171792 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BSD3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.115α = 90
b = 69.938β = 97.36
c = 83.948γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Database references
  • Version 1.3: 2024-03-27
    Changes: Database references