9J5E | pdb_00009j5e

Crystal structure of Hir2_WD40 in complex with Hpc2_NHRD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.193 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the interaction of Hir2 and Hpc2 in the yeast Hir histone chaperone complex.

Tseng, C.H.Hsieh, W.L.Chiang, W.T.Hu, N.J.Lin, C.L.

(2025) Structure 33: 1408-1416.e3

  • DOI: https://doi.org/10.1016/j.str.2025.05.003
  • Primary Citation of Related Structures:  
    9J5E

  • PubMed Abstract: 

    The HIRA complex, composed of HIRA, UBN1, and CABIN1 in humans, plays a central role in histone chaperone activity and chromatin regulation by depositing the H3.3 histone variant into nucleosomes. Proper subunit interactions are critical for complex stability and function. In this study, we examine the interaction between Hir2 and Hpc2, the yeast homologs of HIRA and UBN1, using biochemical and structural approaches. We show that the N-terminal to the Hpc2-related domain (NHRD) of Hpc2 binds to the WD40 domain of Hir2, consistent with the human HIRA-UBN1 interaction. The crystal structure of the Hir2_WD40-Hpc2_NHRD complex reveals a seven-bladed β-propeller fold in Hir2_WD40, with Hpc2_NHRD forming an antiparallel β sheet interface. Notably, a unique five-stranded blade in Hir2_WD40, stabilized by proline residue P228, is essential for Hpc2 binding. Mutational analysis confirms key interface residues, providing structural insights into the evolutionary conservation of the HIRA complex.


  • Organizational Affiliation
    • Graduate Institute of Biochemistry, National Chung Hsing University, Taichung 402202, Taiwan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein HIR2373Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HIR2YOR038COR26.31
UniProt
Find proteins for P32480 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32480 
Go to UniProtKB:  P32480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32480
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide from Histone promoter control protein 221Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q01448 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q01448 
Go to UniProtKB:  Q01448
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01448
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.193 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.541α = 90
b = 103.541β = 90
c = 108.503γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-06-11 
  • Deposition Author(s): Lin, C.-L.

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)TaiwanMOST 111 - 2311 - B - 005 - 002 - MY2

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Database references