5XM1: Histone H3mm7

The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4. Determined by X-ray diffraction at 3.45 Å resolution. Released 7 Mar 2018.

Method: X-ray diffraction
Resolution: 3.45 Å
Organisms: Mus musculus, Homo sapiens
Chains: 10
Atoms: 11,920
Mol. weight: 202.25 kDa
Released: 7 Mar 2018

Explore 5XM1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5XM1 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.

Chain A: 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	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: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-35	9
β-strand	42-43	2	4
α-helix	47-72	26
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	6
α-helix	113-115	3

Chain D: 5 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	103	1
α-helix	106-121	16

Chain 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	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-35	9
β-strand	42-43	2	9
α-helix	47-72	26
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	3
α-helix	113-115	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	106-123	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3mm7	A, E	protein	139	Mus musculus	P84244 (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 (146-mer)	I, J	DNA	146	Homo sapiens

Sequence of entity 1 (A, E), FASTA

>5XM1_1 Histone H3mm7 (chains A, E)
GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPSIGGVKKPHRYRPGTVALREIRRYQK
ATELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>5XM1_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>5XM1_3 Histone H2A type 1-B (chains C, G)
GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL
PKKTESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>5XM1_4 Histone H2B type 3-A (chains D, H)
GSHMPEPSRSTPAPKKGSKKAITKAQKKDGKKRKRGRKESYSIYVYKVLKQVHPDTGISS
KAMGIMNSFVNDIFERIASEASRLAHYNKRSTITSREVQTAVRLLLPGELAKHAVSEGTK
AVTKYTSSK

Sequence of entity 5 (I, J), FASTA

>5XM1_5 DNA (146-MER) (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Primary citation

Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration. Harada, A., Maehara, K., Ono, Y. et al. Nat Commun (2018) 9:1400-1400. DOI 10.1038/s41467-018-03845-1 · PubMed

Other PDB entries of the same protein (UniProt P84244 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PKJ 2.5 Å, Cryo-EM structure of the nucleosome containing Nr5a2 motif at SHL+5.5
8PKI 2.58 Å, Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5
5XM0 2.87 Å, The mouse nucleosome structure containing H2A, H2B type3-A, H3.3, and H4
2RVN Solution structure of the chromodomain of HP1a with the phosphorylated N-terminal tail…

Browse structure collections

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