7PFU: Histone H3.2

Nucleosome stack of the 4x207 nucleosome array containing H1. Determined by electron microscopy at 5.0 Å resolution. Released 3 Aug 2022.

Method: Electron microscopy
Resolution: 5.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 20
Atoms: 27,760
Mol. weight: 783.38 kDa
Released: 3 Aug 2022

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

Secondary structure: helices and β-sheets

7PFU contains 84 α-helices and 46 β-strands across 18 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.

Chains A and E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
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: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77	1	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	1	5
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	105-122	18

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	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	97-98	2	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
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	80-88	9
α-helix	91-96	6
β-strand	101-102	2	3

Chains H and R: 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

Chain K: 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	12
α-helix	86-113	28
β-strand	118	1	13
α-helix	121-131	11

8 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.2	A, E, K, O	protein	136	Homo sapiens	Q71DI3 (AlphaFold model)
Histone H4	B, F, L, P	protein	103	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G, M, Q	protein	147	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-K	D, H, N, R	protein	126	Homo sapiens	O60814 (AlphaFold model)
Histone H1.4	S, U	protein	218	Homo sapiens	P10412
DNA (591-mer)	I	DNA	828	synthetic construct
DNA (591-mer)	J	DNA	828	synthetic construct

Sequence of entity 1 (A, E, K, O), FASTA

>7PFU_1 Histone H3.2 (chains A, E, K, O)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F, L, P), FASTA

>7PFU_2 Histone H4 (chains B, F, L, P)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G, M, Q), FASTA

>7PFU_3 Histone H2A type 1-B/E (chains C, G, M, Q)
HHHHHHENLYFQSNAPWMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSER
VGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTI
AQGGVLPNIQAVLLPKKTESHHKAKGK

Sequence of entity 4 (D, H, N, R), FASTA

>7PFU_4 Histone H2B type 1-K (chains D, H, N, R)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 5 (S, U), FASTA

>7PFU_5 Histone H1.4 (chains S, U)
SETAPAAPAAPAPAEKTPVKKKARKSAGAAKRKASGPPVSELITKAVAASKERSGVSLAA
LKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEAKPKAK
KAGAAKAKKPAGAAKKPKKATGAATPKKSAKKTPKKAKKPAAAAGAKKAKSPKKAKAAKP
KKAPKSPAKAKAVKPKAAKPKTAKPKAAKPKKAAAKKK

Sequence of entity 6 (I), FASTA

>7PFU_6 DNA (591-MER) (chains I)
ATCCTGGCCGCCACTGGCCGCCACTGGCCACTGGAGAATCCCGGTGCCGAGGCCGCTCAA
TTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTA
ACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCACATATATACATCCTGTGCA
TGTAAGTGCATGTAAGTGCATGTAAGTACTCTGGCCGCCACTGGCCGCCACTGGCCACTG
GAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACG
CACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGC
ACGTGTCACATATATACATCCTGTGCATGTAAGTGCATGTAAGTGCATGTAAGTACTCTG
GCCGCCACTGGCCGCCACTGGCCACTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTC
GTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCC
AAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCACATATATACATCCTGTGCATGTAAG
TGCATGTAAGTGCATGTAAGTACTCTGGCCGCCACTGGCCGCCACTGGCCACTGGAGAAT
CCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTA
CGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGT
CACATATATACATCCTGTGCATGTAAGTGCATGTAAGTGCATGTAGAT

Sequence of entity 7 (J), FASTA

>7PFU_7 DNA (591-MER) (chains J)
ATCTACATGCACTTACATGCACTTACATGCACAGGATGTATATATGTGACACGTGCCTGG
AGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTA
AGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGTGG
CCAGTGGCGGCCAGTGGCGGCCAGAGTACTTACATGCACTTACATGCACTTACATGCACA
GGATGTATATATGTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAAC
GCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGC
GGCCTCGGCACCGGGATTCTCCAGTGGCCAGTGGCGGCCAGTGGCGGCCAGAGTACTTAC
ATGCACTTACATGCACTTACATGCACAGGATGTATATATGTGACACGTGCCTGGAGACTA
GGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGT
GCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGTGGCCAGTG
GCGGCCAGTGGCGGCCAGAGTACTTACATGCACTTACATGCACTTACATGCACAGGATGT
ATATATGTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGG
GACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTC
GGCACCGGGATTCTCCAGTGGCCAGTGGCGGCCAGTGGCGGCCAGGAT

Primary citation

Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory. Dombrowski, M., Engeholm, M., Dienemann, C. et al. Nat Struct Mol Biol (2022) 29:493-501. DOI 10.1038/s41594-022-00768-w · 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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