9CDW: HP1alpha chromoshadow domain

Crystal structure of HP1alpha chromoshadow domain in complex with KAP1 peptide. Determined by X-ray diffraction at 2.4 Å resolution. Released 11 Jun 2025.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 6
Atoms: 2,221
Mol. weight: 31.05 kDa
Released: 11 Jun 2025

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

Secondary structure: helices and β-sheets

9CDW contains 16 α-helices and 22 β-strands across 6 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, 5 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	147	1	2
β-strand	148-152	5	1
α-helix	153-159	7
α-helix	161-169	9
β-strand	172-173	2	3

Chain B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	112	1	4
α-helix	116-119	4
α-helix	121-122	2
β-strand	123-130	8	5
β-strand	137-142	6	5
β-strand	147	1	6
β-strand	148-152	5	5
α-helix	153-159	7
α-helix	161-170	10
β-strand	172-173	2	7

Chain C: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	112	1	2
α-helix	116-119	4
α-helix	121-122	2
β-strand	123-130	8	8
β-strand	137-142	6	8
β-strand	148-152	5	8
α-helix	153-159	7
α-helix	161-169	9

Chain D: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	112	1	6
α-helix	117-119	3
α-helix	121-122	2
β-strand	123-130	8	9
β-strand	137-142	6	9
β-strand	147	1	4
β-strand	148-152	5	9
α-helix	153-159	7
α-helix	161-170	10

Chains E and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	488-489	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromobox protein homolog 5	A, B, C, D	protein	64	Homo sapiens	P45973 (AlphaFold model)
Transcription intermediary factor 1-beta peptide	E, F	protein	6	Homo sapiens	Q13263 (AlphaFold model)

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

>9CDW_1 Chromobox protein homolog 5 (chains A, B, C, D)
NDIARGFERGLEPEKIIGATDSCGDLMFLMKWKDTDEADLVLAKEANVKCPQIVIAFYEE
RLTW

Sequence of entity 2 (E, F), FASTA

>9CDW_2 Transcription intermediary factor 1-beta peptide (chains E, F)
VPRVSL

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…
9CEA 2.15 Å, Crystal structure of HP1alpha chromoshadow domain
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

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