9K40: Histone H3.1

Cryo-EM structure of Arabidopsis thaliana H2A-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry). Determined by electron microscopy at 3.15 Å resolution. Released 14 May 2025.

Method: Electron microscopy
Resolution: 3.15 Å
Organism: Arabidopsis thaliana
Chains: 10
Atoms: 11,824
Mol. weight: 204.44 kDa
Released: 14 May 2025

Explore 9K40 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9K40 contains 39 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	45-56	12
α-helix	64-76	13
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	25-28	4
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	97-98	2	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	28-37	10
β-strand	43-44	2	4
α-helix	48-73	26
β-strand	78-79	2	5
α-helix	81-90	10
α-helix	92-97	6
β-strand	102-103	2	6
α-helix	114-116	3

Chains D and H: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	56-58	3
α-helix	61-71	11
β-strand	76-77	2	5
α-helix	79-106	28
β-strand	111-112	2	4
α-helix	114-124	11
α-helix	127-146	20

Chain F: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
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	97-98	2	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	28-37	10
β-strand	43-44	2	9
α-helix	48-74	27
β-strand	78-79	2	10
α-helix	81-90	10
α-helix	92-97	6
β-strand	102-103	2	3
α-helix	114-116	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.1	A, E	protein	136	Arabidopsis thaliana	P59226 (AlphaFold model)
Histone H4	B, F	protein	103	Arabidopsis thaliana	P59259 (AlphaFold model)
Histone H2A.6	C, G	protein	130	Arabidopsis thaliana	Q9LD28 (AlphaFold model)
Histone H2B.1	D, H	protein	148	Arabidopsis thaliana	Q9LQQ4 (AlphaFold model)
15.2.2 DNA (147-mer)	I	DNA	147	Arabidopsis thaliana
15.2.2 DNA (147-mer)	J	DNA	147	Arabidopsis thaliana

Sequence of entity 1 (A, E), FASTA

>9K40_1 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9K40_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9K40_3 Histone H2A.6 (chains C, G)
MAGRGKTLGSGGAKKATSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLAAVLEYL
AAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGDVTIANGGVMPNIHNLLLPK
KAGASKPQED

Sequence of entity 4 (D, H), FASTA

>9K40_4 Histone H2B.1 (chains D, H)
MAPRAEKKPAEKKTAAERPVEENKAAEKAPAEKKPKAGKKLPPKEAGDKKKKRSKKNVET
YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQT
AVRLVLPGELAKHAVSEGTKAVTKFTSS

Sequence of entity 5 (I), FASTA

>9K40_5 15.2.2 DNA (147-MER) (chains I)
ACCTTTATTGACTCCATAATTGACCAATTGAGCGGCTCGATTCAACTGTCAATAACTTCA
AATGAAGCAAGAGCCTTATCGTATTCTCCGCACGATGGTGCTTTAATCCACCGCAACTTT
CCTCTTTAATAAAGGCACAAGCATTAA

Sequence of entity 6 (J), FASTA

>9K40_6 15.2.2 DNA (147-MER) (chains J)
TTAATGCTTGTGCCTTTATTAAAGAGGAAAGTTGCGGTGGATTAAAGCACCATCGTGCGG
AGAATACGATAAGGCTCTTGCTTCATTTGAAGTTATTGACAGTTGAATCGAGCCGCTCAA
TTGGTCAATTATGGAGTCAATAAAGGT

Primary citation

Structural and functional interrelationships of histone H2A with its variants H2A.Z and H2A.W in Arabidopsis. Wang, Y., Wu, J., Yang, S. et al. Structure (2025) 33:1240. DOI 10.1016/j.str.2025.04.015 · PubMed

Other PDB entries of the same protein (UniProt P59226 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6LQF 1.5 Å, Crystal structure of Arabidopsis ARID5 ARID-PHD cassette in complex with H3K4me3 peptide…
5YVX 1.59 Å, Crystal structure of SDG8 CW domain in complex with H3K4me1 peptide
9M4S 1.6 Å, crystal structure of Arabidopsis thaliana ING2 PHD finger in complex with an H3K4me3…
9M4R 1.7 Å, crystal structure of Arabidopsis thaliana ING1 PHD finger in complex with an H3K4me3…
7DE9 1.71 Å, crystal structure of Arabidopsis RDM15 tudor domain in complex with an H3K4me1 peptide
5ZWX 1.9 Å, Crystal structure of Raphanus sativus AGDP1 AGD12 in complex with an H3K9me2 peptide
6LQE 1.9 Å, Crystal structure of Arabidopsis ARID5 PHD finger in complex with H3K4me3 peptide
5HH7 1.9 Å, crystal structure of Arabidopsis ORC1b BAH-PHD cassette in complex with unmodified H3…
5Z8L 2.0 Å, crystal structure of Arabidopsis thaliana EBS in complex with an H3K27me3 peptide
5VBC 2.1 Å, Crystal structure of ATXR5 in complex with histone H3.1
8JG4 2.3 Å, Crystal Structure of YAF9A YEATS bound to H3K27cr peptide
7YTA 2.31 Å, crystal structure of NtAGDP3 AGD1-2 in complex with an H3K9me2 peptide

Browse structure collections

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