9K45: Histone H3.3

Cryo-EM structure of Arabidopsis thaliana H2A.Z-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry). Determined by electron microscopy at 2.71 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 2.71 Å
Organism: Arabidopsis thaliana
Chains: 10
Atoms: 11,830
Mol. weight: 205.96 kDa
Released: 12 Nov 2025

Explore 9K45 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9K45 contains 36 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-54	10
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

Chains B and F: 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	97-98	2	3

Chain C: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	28-32	5
α-helix	38-48	11
β-strand	54-55	2	4
α-helix	57-84	28
β-strand	89-90	2	5
α-helix	92-100	9
α-helix	103-108	6
α-helix	111	1
β-strand	112-113	2	6
α-helix	124-126	3

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

Element	Residues	Length	Sheet
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 G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	28-32	5
α-helix	38-48	11
β-strand	54-55	2	9
α-helix	57-84	28
β-strand	89-90	2	10
α-helix	92-100	9
α-helix	103-108	6
β-strand	112-113	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.3	A, E	protein	136	Arabidopsis thaliana	P59169 (AlphaFold model)
Histone H4	B, F	protein	103	Arabidopsis thaliana	P59259 (AlphaFold model)
Probable histone H2A variant 3	C, G	protein	134	Arabidopsis thaliana	Q9C944 (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

>9K45_1 Histone H3.3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9K45_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9K45_3 Probable histone H2A variant 3 (chains C, G)
MSGKGAKGLIMGKPSGSDKDKDKKKPITRSSRAGLQFPVGRVHRLLKTRSTAHGRVGATA
AVYTAAILEYLTAEVLELAGNASKDLKVKRISPRHLQLAIRGDEELDTLIKGTIAGGGVI
PHIHKSLINKSAKE

Sequence of entity 4 (D, H), FASTA

>9K45_4 Histone H2B.1 (chains D, H)
MAPRAEKKPAEKKTAAERPVEENKAAEKAPAEKKPKAGKKLPPKEAGDKKKKRSKKNVET
YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQT
AVRLVLPGELAKHAVSEGTKAVTKFTSS

Sequence of entity 5 (I), FASTA

>9K45_5 15.2.2 DNA (147-MER) (chains I)
ACCTTTATTGACTCCATAATTGACCAATTGAGCGGCTCGATTCAACTGTCAATAACTTCA
AATGAAGCAAGAGCCTTATCGTATTCTCCGCACGATGGTGCTTTAATCCACCGCAACTTT
CCTCTTTAATAAAGGCACAAGCATTAA

Sequence of entity 6 (J), FASTA

>9K45_6 15.2.2 DNA (147-MER) (chains J)
TTAATGCTTGTGCCTTTATTAAAGAGGAAAGTTGCGGTGGATTAAAGCACCATCGTGCGG
AGAATACGATAAGGCTCTTGCTTCATTTGAAGTTATTGACAGTTGAATCGAGCCGCTCAA
TTGGTCAATTATGGAGTCAATAAAGGT

Primary citation

Functional redundancy of core histone H2A and its variants in Arabidopsis. Wang, Y., Dong, A. To be published.

Other PDB entries of the same protein (UniProt P59169 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4PLI 1.65 Å, Structure of the chromodomain of MRG2 in complex with H3K36me3
4PL6 1.68 Å, Structure of the chromodomain of MRG2 in complex with H3K4me3
8XAG 1.75 Å, Crystal structure of the chromodomain of Arabidopsis LHP1 in complex with histone…
4PLL 2.6 Å, Structure of the chromodaomain of MRG2 in complex with H3K36me3
9K46 2.85 Å, Cryo-EM structure of Arabidopsis thaliana H2A.W-H3.3-nucleosome with Arabidopsis native…
7UX9 3.2 Å, Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA)
9K44 3.22 Å, Cryo-EM structure of Arabidopsis thaliana H2A-H3.3-nucleosome with Arabidopsis native…

Browse structure collections

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