3AV1: Histone H3.2

The human nucleosome structure containing the histone variant H3.2. Determined by X-ray diffraction at 2.5 Å resolution. Released 1 Jun 2011.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 10
Atoms: 12,050
Mol. weight: 202.2 kDa
Released: 1 Jun 2011

Explore 3AV1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3AV1 contains 38 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	97-98	2	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

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	104-122	19

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	121-130	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
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	46-71	26
β-strand	77-78	2	10
α-helix	80-88	9
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	104-123	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.2	A, E	protein	139	Homo sapiens	Q71DI3 (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)
146-mer DNA	I, J	DNA	146

Sequence of entity 1 (A, E), FASTA

>3AV1_1 Histone H3.2 (chains A, E)
GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQK
STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>3AV1_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>3AV1_3 Histone H2A type 1-B/E (chains C, G)
GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL
PKKTESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>3AV1_4 Histone H2B type 1-J (chains D, H)
GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISS
KAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTK
AVTKYTSAK

Sequence of entity 5 (I, J), FASTA

>3AV1_5 146-MER DNA (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Primary citation

Structures of human nucleosomes containing major histone H3 variants. Tachiwana, H., Osakabe, A., Shiga, T. et al. Acta Crystallogr D Biol Crystallogr (2011) 67:578-583. DOI 10.1107/S0907444911014818 · PubMed

Other PDB entries of the same protein (UniProt Q71DI3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2X4W 1.5 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4MZG 1.7 Å, Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide
2X4Y 1.7 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
2X4X 1.85 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4OUC 1.9 Å, Structure of human haspin in complex with histone H3 substrate
5VAC 1.95 Å, Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
6ACE 1.98 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
7UVA 1.98 Å, Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36…
5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide

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