9ECP: Native human NCP purified from HEK293 cells

Structure of the native human NCP purified from HEK293 cells. Determined by electron microscopy at 1.91 Å resolution. Released 22 Oct 2025.

Method: Electron microscopy
Resolution: 1.91 Å
Organism: Homo sapiens
Chains: 10
Atoms: 12,239
Mol. weight: 175.42 kDa
Released: 22 Oct 2025

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

Secondary structure: helices and β-sheets

9ECP contains 40 α-helices and 20 β-strands across 8 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.

Chains A and E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-55	11
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	96-98	3	3

Chain C: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	6
α-helix	113-115	3

Chains D and H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	39-49	11
β-strand	54-55	2	5
α-helix	57-84	28
β-strand	89-90	2	4
α-helix	92-102	11
α-helix	105-124	20

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-98	3	6

Chain G: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	46-72	27
β-strand	77-78	2	10
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	3
α-helix	113-115	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.1	A, E	protein	96	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B, F	protein	82	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 3	C, G	protein	109	Homo sapiens	Q7L7L0 (AlphaFold model)
Histone H2B type 1-K	D, H	protein	94	Homo sapiens	O60814 (AlphaFold model)
DNA (145-mer)	I, J	DNA	145	Homo sapiens

Sequence of entity 1 (A, E), FASTA

>9ECP_1 Histone H3.1 (chains A, E)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACE
AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE

Sequence of entity 2 (B, F), FASTA

>9ECP_2 Histone H4 (chains B, F)
VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT
VTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9ECP_3 Histone H2A type 3 (chains C, G)
ARAKAKSRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNA
ARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK

Sequence of entity 4 (D, H), FASTA

>9ECP_4 Histone H2B type 1-K (chains D, H)
RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA

Sequence of entity 5 (I, J), FASTA

>9ECP_5 DNA (145-MER) (chains I, J)
ATCACAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGGATTCCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTGTGAT

Primary citation

The structure and composition of native human nucleosomes. Reid, X.J., Sobti, M., Zeng, Y.C. et al. bioRxiv (2025). DOI 10.1101/2025.10.10.681767

Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail

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