9ZEO: Histone H3.1

Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1. Determined by electron microscopy at 3.1 Å resolution. Released 4 Mar 2026.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: artificial sequences, Homo sapiens
Chains: 11
Atoms: 12,895
Mol. weight: 190.35 kDa
Released: 4 Mar 2026

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

Secondary structure: helices and β-sheets

9ZEO contains 35 α-helices and 36 β-strands across 9 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-54	10
α-helix	64-78	15
β-strand	83-84	2	1
α-helix	88-113	26
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	31-41	11
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: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	28-35	8
β-strand	43	1	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	92-96	5
β-strand	100-102	3	6

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	5
α-helix	56-83	28
β-strand	89	1	4
α-helix	91-101	11
α-helix	104-124	21

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-54	10
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	88-113	26
β-strand	118-119	2	8
α-helix	121-131	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45-46	2	8
α-helix	51-75	25
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-98	3	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	28-35	8
β-strand	42-43	2	9
α-helix	46-71	26
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	93-96	4
β-strand	100-102	3	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	10
α-helix	56-83	28
β-strand	88-89	2	9
α-helix	91-101	11
α-helix	104-121	18

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA Tracking Strand	I	DNA	145	artificial sequences
DNA Lagging Strand	J	DNA	145	artificial sequences
Histone H3.1	A, E	protein	98	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B, F	protein	83	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G	protein	111	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-K	D, H	protein	95	Homo sapiens	O60814 (AlphaFold model)
Single-chain antibody (VHH) 1G1	K	protein	124	Homo sapiens

Sequence of entity 1 (I), FASTA

>9ZEO_1 DNA Tracking Strand (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT

Sequence of entity 2 (J), FASTA

>9ZEO_2 DNA Lagging Strand (chains J)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTGAT

Sequence of entity 3 (A, E), FASTA

>9ZEO_3 Histone H3.1 (chains A, E)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACE
AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 4 (B, F), FASTA

>9ZEO_4 Histone H4 (chains B, F)
KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK
TVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (C, G), FASTA

>9ZEO_5 Histone H2A type 1-B/E (chains C, G)
ARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNA
ARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT

Sequence of entity 6 (D, H), FASTA

>9ZEO_6 Histone H2B type 1-K (chains D, H)
RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Sequence of entity 7 (K), FASTA

>9ZEO_7 Single-chain antibody (VHH) 1G1 (chains K)
AEVQLVESGGGLVQAGGSLSVSCTASGRTVSSYAMGWFRQAPGKEREFVAGISRRGSRTY
YVDSVEGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAVRSRGSDYGQIDSYGYWGQGTQ
VTVS

Primary citation

Different modes of engagement with the nucleosome acidic patch yield distinct functional outcomes. Chakraborty, U., Saccone, E.C., Cruz-Becerra, G. et al. Nucleic Acids Res (2026) 54. DOI 10.1093/nar/gkag693 · PubMed

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

Browse structure collections

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