5X7X: Nucleosome containing H3.3

The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution. Determined by X-ray diffraction at 2.18 Å resolution. Released 19 Apr 2017.

Method: X-ray diffraction
Resolution: 2.18 Å
Organism: Homo sapiens
Chains: 10
Atoms: 12,392
Mol. weight: 202.93 kDa
Ligands: MN
Released: 19 Apr 2017

Explore 5X7X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5X7X contains 40 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: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	6
α-helix	113-115	3

Chains D and H: 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	104-122	19

Chain E: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	37-39	3
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 F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-22	4
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-98	3	6

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	46-72	27
β-strand	77-78	2	10
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	3
α-helix	113-115	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.3	A, E	protein	139	Homo sapiens	P84243 (AlphaFold model)
Histone H4	B, F	protein	106	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G	protein	133	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-J	D, H	protein	129	Homo sapiens	P06899 (AlphaFold model)
DNA (146-mer)	I, J	DNA	146	Homo sapiens

Sequence of entity 1 (A, E), FASTA

>5X7X_1 Histone H3.3 (chains A, E)
GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQK
STELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>5X7X_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>5X7X_3 Histone H2A type 1-B/E (chains C, G)
GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL
PKKTESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>5X7X_4 Histone H2B type 1-J (chains D, H)
GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISS
KAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTK
AVTKYTSAK

Sequence of entity 5 (I, J), FASTA

>5X7X_5 DNA (146-MER) (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	13

Water and common crystallization additives (CL) are not listed.

Primary citation

Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8. Taguchi, H., Xie, Y., Horikoshi, N. et al. Biochemistry (2017) 56:2184-2196. DOI 10.1021/acs.biochem.6b01098 · PubMed

Other PDB entries of the same protein (UniProt P84243 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3QL9 0.93 Å, Monoclinic complex structure of ATRX ADD bound to histone H3K9me3 peptide
4GNE 1.47 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-7
4L58 1.48 Å, Crystal structure of the MLL5 PHD finger in complex with H3K4me3
5JLB 1.5 Å, Crystal structure of SETD2 bound to histone H3.3 K36I peptide
4GNF 1.55 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-15
3QLA 1.6 Å, Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide
3MUL 1.65 Å, Crystal structure of Brd4 bromodomain 1 with butyrylated histone H3-K(buty)14
9G4A 1.65 Å, Structure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide
4GNG 1.73 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide
3MUK 1.75 Å, Crystal structure of Brd4 bromodomain 1 with propionylated histone H3-K(prop)23
4QQ4 1.75 Å, CW-type zinc finger of MORC3 in complex with the amino terminus of histone H3
1PDQ 1.76 Å, Polycomb chromodomain complexed with the histone H3 tail containing trimethyllysine 27.

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