9CEA | pdb_00009cea

Crystal structure of HP1alpha chromoshadow domain

• PDB DOI: https://doi.org/10.2210/pdb9CEA/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-26 Released: 2025-06-11 
• Deposition Author(s): Selvam, K., Gaurav, N., Kutateladze, T.G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.277 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.227 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

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

• PubMed: 40450002 
• DOI: https://doi.org/10.1038/s41467-025-60279-2
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.
Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
Department of Biology II, Ludwig-Maximilians-Universität München, München, Germany.
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
Department of Biology, Technical University of Darmstadt, Darmstadt, Germany.
Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan.
Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
Graduate School of Science and Engineering, Chiba University, Chiba, Japan.
Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA. [e-mail].
Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, USA. [e-mail].
Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.89 kDa 
• Atom Count: 1,991 
• Modeled Residue Count: 243 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromobox protein homolog 5	A, B, C, D	63	Homo sapiens	Mutation(s): 0  Gene Names: CBX5, HP1A
UniProt & NIH Common Fund Data Resources
Find proteins for P45973 (Homo sapiens) Explore P45973  Go to UniProtKB:  P45973
PHAROS:  P45973 GTEx:  ENSG00000094916

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.277 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.227 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39CEA

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.758	α = 90
b = 66.854	β = 90
c = 70.908	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Selvam, K., Gaurav, N., Kutateladze, T.G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release