7DBH: The mouse nucleosome structure containing H3mm18

The mouse nucleosome structure containing H3mm18. Determined by electron microscopy at 3.6 Å resolution. Released 19 Jan 2022.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Mus musculus
Chains: 10
Atoms: 10,631
Mol. weight: 201.08 kDa
Released: 19 Jan 2022

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

Secondary structure: helices and β-sheets

7DBH contains 33 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: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	64-76	13
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-130	10

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	48-75	28
β-strand	80-81	2	1
α-helix	83-93	11
β-strand	97-98	2	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	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	88-89	2	4
α-helix	91-101	11
α-helix	104-123	20

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	49-56	8
α-helix	64-78	15
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	31-40	10
β-strand	45-46	2	8
α-helix	48-75	28
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	17-21	5
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	46-72	27
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	91-97	7
β-strand	101-102	2	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	104-122	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3mm18	A, E	protein	139	Mus musculus	A0A8X6EH29 (AlphaFold model)
Histone H4	B, F	protein	106	Mus musculus	P62806 (AlphaFold model)
Histone H2A type 1-B	C, G	protein	133	Mus musculus	C0HKE1 (AlphaFold model)
Histone H2B type 3-A	D, H	protein	129	Mus musculus	Q9D2U9 (AlphaFold model)
DNA (126-mer)	I	DNA	145	Mus musculus
DNA (126-mer)	J	DNA	145	Mus musculus

Sequence of entity 1 (A, E), FASTA

>7DBH_1 Histone H3mm18 (chains A, E)
GSHMARTKQTARKSTGDKAPRKQLATKAARKSAPSTGGVKKPHCYRPGTVALREIRSYQK
SSELLIRKLPFQRLVLEIAQDFKTDLCFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKR
VTIMPKDTQLAGYICRECA

Sequence of entity 2 (B, F), FASTA

>7DBH_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>7DBH_3 Histone H2A type 1-B (chains C, G)
GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL
PKKTESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>7DBH_4 Histone H2B type 3-A (chains D, H)
GSHMPEPSRSTPAPKKGSKKAITKAQKKDGKKRKRGRKESYSIYVYKVLKQVHPDTGISS
KAMGIMNSFVNDIFERIASEASRLAHYNKRSTITSREVQTAVRLLLPGELAKHAVSEGTK
AVTKYTSSK

Sequence of entity 5 (I), FASTA

>7DBH_5 DNA (126-MER) (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT

Sequence of entity 6 (J), FASTA

>7DBH_6 DNA (126-MER) (chains J)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTGAT

Primary citation

Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant. Hirai, S., Tomimatsu, K., Miyawaki-Kuwakado, A. et al. Nucleic Acids Res (2022) 50:72-91. DOI 10.1093/nar/gkab1137 · PubMed

Other PDB entries of the same protein (UniProt A0A8X6EH29 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7VBM 3.4 Å, The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv

Browse structure collections

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