9B3P: H2A.Z-H3.3 double-variant nucleosome

The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome. Determined by electron microscopy at 3.0 Å resolution. Released 12 Jun 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, Xenopus laevis, Mus musculus
Chains: 10
Atoms: 11,067
Mol. weight: 205.48 kDa
Released: 12 Jun 2024

Explore 9B3P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B3P contains 37 α-helices and 16 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, 1 β-strand

Element	Residues	Length	Sheet
α-helix	45-49	5
α-helix	51-54	4
α-helix	65-78	14
β-strand	83-84	2	1
α-helix	86-113	28
α-helix	122-131	10

Chain B: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-41	11
α-helix	50-74	25
β-strand	80-81	2	1
α-helix	84-93	10
β-strand	97	1	2

Chain C: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-23	5
α-helix	29-39	11
β-strand	45-46	2	3
α-helix	48-73	26
α-helix	81-82	2
α-helix	83-91	9
α-helix	95-99	5
β-strand	103	1	4

Chain D: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	41-48	8
α-helix	56-82	27
β-strand	88-89	2	3
α-helix	91-101	11
α-helix	106-122	17

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	51-54	4
α-helix	65-78	14
β-strand	83-84	2	5
α-helix	86-113	28
β-strand	119	1	6
α-helix	121-131	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-38	8
β-strand	46	1	6
α-helix	50-74	25
β-strand	80-81	2	5
α-helix	84-93	10
β-strand	97	1	4

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-23	5
α-helix	29-36	8
β-strand	45-46	2	7
α-helix	48-72	25
β-strand	80	1	8
α-helix	81-82	2
α-helix	83-91	9
β-strand	103	1	2
α-helix	115-117	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-48	8
β-strand	53	1	8
α-helix	56-83	28
β-strand	88-89	2	7
α-helix	91-101	11
α-helix	106-122	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.3	A, E	protein	136	Homo sapiens	P84243 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A.Z	C, G	protein	128	Mus musculus	P0C0S6 (AlphaFold model)
Histone H2B 1.1	D, H	protein	126	Xenopus laevis	P02281 (AlphaFold model)
DNA (128-mer)	I	DNA	147	synthetic construct
DNA (128-mer)	J	DNA	167	synthetic construct

Sequence of entity 1 (A, E), FASTA

>9B3P_1 Histone H3.3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9B3P_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9B3P_3 Histone H2A.Z (chains C, G)
MAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILE
YLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIG
KKGQQKTV

Sequence of entity 4 (D, H), FASTA

>9B3P_4 Histone H2B 1.1 (chains D, H)
MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 5 (I), FASTA

>9B3P_5 DNA (128-MER) (chains I)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG

Sequence of entity 6 (J), FASTA

>9B3P_6 DNA (128-MER) (chains J)
ATCCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCA
CCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCT
AGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGACTAGAT

Primary citation

Structural and Biochemical Characterization of the Nucleosome Containing Variants H3.3 and H2A.Z. Jung, H., Sokolova, V., Lee, G. et al. Epigenomes (2024) 8. DOI 10.3390/epigenomes8020021 · 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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