9CEA: HP1alpha chromoshadow domain

Crystal structure of HP1alpha chromoshadow domain. Determined by X-ray diffraction at 2.15 Å resolution. Released 11 Jun 2025.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 4
Atoms: 1,991
Mol. weight: 28.89 kDa
Released: 11 Jun 2025

Explore 9CEA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CEA contains 16 α-helices and 12 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	116-119	4
α-helix	121-122	2
β-strand	123-130	8	1
β-strand	137-142	6	1
β-strand	149-152	4	1
α-helix	153-159	7
α-helix	161-171	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	116-119	4
α-helix	121-122	2
β-strand	123-130	8	2
β-strand	137-142	6	2
β-strand	149-152	4	2
α-helix	153-159	7
α-helix	161-172	12

Chain C: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	116-119	4
α-helix	121-122	2
β-strand	123-132	10	3
β-strand	135-142	8	3
β-strand	149-152	4	3
α-helix	153-159	7
α-helix	161-171	11

Chain D: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	116-119	4
α-helix	121-122	2
β-strand	123-132	10	4
β-strand	135-142	8	4
β-strand	149-152	4	4
α-helix	153-159	7
α-helix	161-170	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromobox protein homolog 5	A, B, C, D	protein	63	Homo sapiens	P45973 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9CEA_1 Chromobox protein homolog 5 (chains A, B, C, D)
IARGFERGLEPEKIIGATDSCGDLMFLMKWKDTDEADLVLAKEANVKCPQIVIAFYEERL
TWH

Primary citation

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. et al. Nat Commun (2025) 16:5066-5066. DOI 10.1038/s41467-025-60279-2 · PubMed

Other PDB entries of the same protein (UniProt P45973 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FDT 2.0 Å, Crystal structure of the complex of human chromobox homolog 5 (CBX5) with H3K9(me)3…
9CDW 2.4 Å, Crystal structure of HP1alpha chromoshadow domain in complex with KAP1 peptide
3I3C 2.48 Å, Crystal Structural of CBX5 Chromo Shadow Domain
9CMT 3.17 Å, The crystal structure of HP1alpha CSD-Agno complex
8UXQ 6.3 Å, Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome

Browse structure collections

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