9CEA | pdb_00009cea

Crystal structure of HP1alpha chromoshadow domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.277 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The HP1 box of KAP1 organizes HP1 alpha for silencing of endogenous retroviral elements in embryonic stem cells.

Gaurav, N.O'Hara, R.Hyder, U.Qin, W.Her, C.Romero, H.Kumar, A.Marcaida, M.J.Singh, R.K.Hovius, R.Selvam, K.Liu, J.Martire, S.Yao, Y.Challa, A.Dal Peraro, M.Fierz, B.Kono, H.Cardoso, M.C.Debelouchina, G.T.Leonhardt, H.D'Orso, I.Banaszynski, L.A.Kutateladze, T.G.

(2025) Nat Commun 16: 5066-5066

  • DOI: https://doi.org/10.1038/s41467-025-60279-2
  • Primary Citation of Related Structures:  
    9CDW, 9CEA

  • PubMed Abstract: 

    Repression of endogenous retroviral elements (ERVs) is facilitated by KAP1 (KRAB-associated protein 1)-containing complexes, however the underlying mechanism remains unclear. Here, we show that binding of KAP1 to the major component of the heterochromatin spreading and maintenance network, HP1α, plays a critical role in silencing of repetitive elements. Structural, biochemical and mutagenesis studies demonstrate that the association of the HP1 box of KAP1 (KAP1 Hbox ) with the chromoshadow domain of HP1α (HP1α CSD ) leads to a symmetrical arrangement of HP1α CSD and multimerization that may promote the closed state of chromatin. The formation of the KAP1 Hbox -HP1α CSD complex enhances charge driven DNA binding and phase separation activities of HP1α. ChIP-seq and ATAC-seq analyses using KAP1 knock out mouse embryonic stem cells expressing wild type KAP1 or HP1-deficient KAP1 mutant show that in vivo, KAP1 engagement with HP1 is required for maintaining inaccessible chromatin at ERVs. Our findings provide mechanistic and functional insights that further our understanding of how ERVs are silenced.


  • Organizational Affiliation
    • Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromobox protein homolog 5
A, B, C, D
63Homo sapiensMutation(s): 0 
Gene Names: CBX5HP1A
UniProt & NIH Common Fund Data Resources
Find proteins for P45973 (Homo sapiens)
Explore P45973 
Go to UniProtKB:  P45973
PHAROS:  P45973
GTEx:  ENSG00000094916 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45973
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.277 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.758α = 90
b = 66.854β = 90
c = 70.908γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

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: 2025-06-11
    Type: Initial release