8J92: Nucleosome containing Arabidopsis thaliana H2A.W

Cryo-EM structure of nucleosome containing Arabidopsis thaliana H2A.W. Determined by electron microscopy at 2.9 Å resolution. Released 3 Jul 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Arabidopsis thaliana, synthetic construct
Chains: 10
Atoms: 12,003
Mol. weight: 225.02 kDa
Released: 3 Jul 2024

Explore 8J92 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8J92 contains 37 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.

Chain A: 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	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: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-30	5
α-helix	36-45	10
β-strand	51-52	2	4
α-helix	56-81	26
β-strand	86-87	2	5
α-helix	89-98	10
α-helix	100-105	6
β-strand	110-111	2	6

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	63-73	11
β-strand	78-79	2	5
α-helix	81-106	26
α-helix	107-109	3
β-strand	113-114	2	4
α-helix	116-126	11
α-helix	129-148	20

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	86-113	28
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	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	97-98	2	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-30	5
α-helix	36-45	10
β-strand	51-52	2	9
α-helix	56-81	26
β-strand	86-87	2	10
α-helix	89-98	10
α-helix	100-105	6
β-strand	109-111	3	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	63-73	11
β-strand	78-79	2	10
α-helix	81-108	28
β-strand	113-114	2	9
α-helix	116-126	11
α-helix	129-148	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.1	A, E	protein	139	Arabidopsis thaliana	P59226 (AlphaFold model)
Histone H4	B, F	protein	106	Arabidopsis thaliana	P59259 (AlphaFold model)
HTA6	C, G	protein	153	Arabidopsis thaliana	Q9FJE8 (AlphaFold model)
HTB9	D, H	protein	153	Arabidopsis thaliana	O23629 (AlphaFold model)
DNA (169-mer)	I	DNA	169	synthetic construct
DNA (169-mer)	J	DNA	169	synthetic construct

Sequence of entity 1 (A, E), FASTA

>8J92_1 Histone H3.1 (chains A, E)
GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQK
STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>8J92_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>8J92_3 HTA6 (chains C, G)
GSHMESTGKVKKAFGGRKPPGAPKTKSVSKSMKAGLQFPVGRITRFLKKGRYAQRLGGGA
PVYMAAVLEYLAAEVLELAGNAARDNKKSRIIPRHLLLAIRNDEELGKLLSGVTIAHGGV
LPNINSVLLPKKSATKPAEEKATKSPVKSPKKA

Sequence of entity 4 (D, H), FASTA

>8J92_4 HTB9 (chains D, H)
GSHMAPRAEKKPAEKKPAAEKPVEEKSKAEKAPAEKKPKAGKKLPKEAGAGGDKKKKMKK
KSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITS
REIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS

Sequence of entity 5 (I), FASTA

>8J92_5 DNA (169-MER) (chains I)
ATCGGACCCTATCGCGAGCCAGGCCTGAGAATCCGGTGCCGAGGCCGCTCAATTGGTCGT
AGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAA
GGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGAT

Sequence of entity 6 (J), FASTA

>8J92_6 DNA (169-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGATTCTCAGGCCTGGCTCGCGATAGGGTCCGAT

Primary citation

Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1. Osakabe, A., Takizawa, Y., Horikoshi, N. et al. Nat Commun (2024) 15:5187-5187. DOI 10.1038/s41467-024-49465-w · 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

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