7UX9: Arabidopsis DDM1

Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA). Determined by electron microscopy at 3.2 Å resolution. Released 9 Aug 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Arabidopsis thaliana, Xenopus laevis, synthetic construct
Chains: 11
Atoms: 15,515
Mol. weight: 296.12 kDa
Released: 9 Aug 2023

Explore 7UX9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UX9 contains 55 α-helices and 28 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.

Chains A and B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	37-45	9
β-strand	51	1	1
α-helix	56-81	26
β-strand	86-87	2	2
α-helix	89-97	9
α-helix	100-105	6
β-strand	109-111	3	3

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

Element	Residues	Length	Sheet
α-helix	63-73	11
β-strand	78-79	2	2
α-helix	81-108	28
β-strand	113	1	1
α-helix	116-126	11
α-helix	130-147	18

Chains E and F: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	86-113	28
α-helix	121-131	11

Chains G and H: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
α-helix	51-75	25
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-98	3	6

Chain P: 23 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	204-218	15
β-strand	223-225	3	9
α-helix	230-246	17
β-strand	253-257	5	9
α-helix	259-261	3
α-helix	262-272	11
β-strand	279-280	2	9
α-helix	285-291	7
β-strand	307-310	4	9
α-helix	319-324	6
β-strand	329-332	4	9
α-helix	345-351	7
β-strand	356-360	5	9
α-helix	371-379	9
α-helix	413-424	12
β-strand	443-450	8	10
α-helix	451-453	3
α-helix	454-463	10
α-helix	468-473	6
α-helix	477	1
α-helix	490-498	9
α-helix	500-506	7
α-helix	516-519	4
α-helix	520-522	3
α-helix	524-536	13
β-strand	543-547	5	10
α-helix	552-563	12
β-strand	567-570	4	10
α-helix	578-583	6
β-strand	595-599	5	10
β-strand	614-617	4	10
α-helix	624-634	11
β-strand	643-650	8	10
α-helix	654-666	13
α-helix	667-669	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable histone H2A.7	A, B	protein	150	Arabidopsis thaliana	Q9FJE8 (AlphaFold model)
Histone H2B	C, D	protein	150	Arabidopsis thaliana	O23629 (AlphaFold model)
Histone H3.3	E, F	protein	136	Arabidopsis thaliana	P59169 (AlphaFold model)
Histone H4	G, H	protein	103	Xenopus laevis	P62799 (AlphaFold model)
ATP-dependent DNA helicase DDM1	P	protein	764	Arabidopsis thaliana	Q9XFH4
DNA (sense strand)	Y	DNA	147	synthetic construct
DNA (antisense strand)	Z	DNA	147	synthetic construct

Sequence of entity 1 (A, B), FASTA

>7UX9_1 Probable histone H2A.7 (chains A, B)
MESTGKVKKAFGGRKPPGAPKTKSVSKSMKAGLQFPVGRITRFLKKGRYAQRLGGGAPVY
MAAVLEYLAAEVLELAGNAARDNKKSRIIPRHLLLAIRNDEELGKLLSGVTIAHGGVLPN
INSVLLPKKSATKPAEEKATKSPVKSPKKA

Sequence of entity 2 (C, D), FASTA

>7UX9_2 Histone H2B (chains C, D)
MAPRAEKKPAEKKPAAEKPVEEKSKAEKAPAEKKPKAGKKLPKEAGAGGDKKKKMKKKSV
ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITSREI
QTAVRLVLPGELAKHAVSEGTKAVTKFTSS

Sequence of entity 3 (E, F), FASTA

>7UX9_3 Histone H3.3 (chains E, F)
MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 4 (G, H), FASTA

>7UX9_4 Histone H4 (chains G, H)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (P), FASTA

>7UX9_5 ATP-dependent DNA helicase DDM1 (chains P)
MVSLRSRKVIPASEMVSDGKTEKDASGDSPTSVLNEEENCEEKSVTVVEEEILLAKNGDS
SLISEAMAQEEEQLLKLREDEEKANNAGSAVAPNLNETQFTKLDELLTQTQLYSEFLLEK
MEDITINGIESESQKAEPEKTGRGRKRKAASQYNNTKAKRAVAAMISRSKEDGETINSDL
TEEETVIKLQNELCPLLTGGQLKSYQLKGVKWLISLWQNGLNGILADQMGLGKTIQTIGF
LSHLKGNGLDGPYLVIAPLSTLSNWFNEIARFTPSINAIIYHGDKNQRDELRRKHMPKTV
GPKFPIVITSYEVAMNDAKRILRHYPWKYVVIDEGHRLKNHKCKLLRELKHLKMDNKLLL
TGTPLQNNLSELWSLLNFILPDIFTSHDEFESWFDFSEKNKNEATKEEEEKRRAQVVSKL
HGILRPFILRRMKCDVELSLPRKKEIIMYATMTDHQKKFQEHLVNNTLEAHLGENAIRGQ
GWKGKLNNLVIQLRKNCNHPDLLQGQIDGSYLYPPVEEIVGQCGKFRLLERLLVRLFANN
HKVLIFSQWTKLLDIMDYYFSEKGFEVCRIDGSVKLDERRRQIKDFSDEKSSCSIFLLST
RAGGLGINLTAADTCILYDSDWNPQMDLQAMDRCHRIGQTKPVHVYRLSTAQSIETRVLK
RAYSKLKLEHVVIGQGQFHQERAKSSTPLEEEDILALLKEDETAEDKLIQTDISDADLDR
LLDRSDLTITAPGETQAAEAFPVKGPGWEVVLPSSGGMLSSLNS

Sequence of entity 6 (Y), FASTA

>7UX9_6 DNA (sense strand) (chains Y)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCACATATATACATCCTGT

Sequence of entity 7 (Z), FASTA

>7UX9_7 DNA (antisense strand) (chains Z)
ACAGGATGTATATATGTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG

Primary citation

Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation. Lee, S.C., Adams, D.W., Ipsaro, J.J. et al. Cell (2023) 186:4100. DOI 10.1016/j.cell.2023.08.001 · PubMed

Other PDB entries of the same protein (UniProt Q9FJE8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9K41 2.81 Å, Cryo-EM structure of Arabidopsis thaliana H2A.W-nucleosome with Arabidopsis native 147bp…
9K46 2.85 Å, Cryo-EM structure of Arabidopsis thaliana H2A.W-H3.3-nucleosome with Arabidopsis native…
8J92 2.9 Å, Cryo-EM structure of nucleosome containing Arabidopsis thaliana H2A.W
8KCC 3.1 Å, Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2
8J90 4.71 Å, Cryo-EM structure of DDM1-nucleosome complex

Browse structure collections

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