7XPX: Histone methyltransferase SET8

Cryo-EM structure of the histone methyltransferase SET8 bound to H4K20Ecx-nucleosome. Determined by electron microscopy at 3.2 Å resolution. Released 1 Jun 2022.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Xenopus laevis, Homo sapiens
Chains: 11
Atoms: 13,408
Mol. weight: 223.41 kDa
Ligands: SAM
Released: 1 Jun 2022

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

Secondary structure: helices and β-sheets

7XPX contains 43 α-helices and 34 β-strands across 9 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: 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	64-75	12
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, 4 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	3
α-helix	25-28	4
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	4

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	27-36	10
β-strand	42-43	2	5
α-helix	46-72	27
β-strand	77-78	2	6
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	7

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	6
α-helix	53-80	28
β-strand	85-86	2	5
α-helix	88-98	11
α-helix	101-119	19

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	8
α-helix	86-113	28
β-strand	118-119	2	9
α-helix	121-131	11

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	9
α-helix	50-75	26
β-strand	80-81	2	8
α-helix	83-92	10
β-strand	96-98	3	7

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	10
α-helix	46-72	27
β-strand	77-78	2	11
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	4

Chain H: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	28-30	3
α-helix	35-45	11
β-strand	50-51	2	11
α-helix	53-80	28
β-strand	85-86	2	10
α-helix	88-98	11
α-helix	102-120	19

1 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	A, E	protein	135	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	102	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	129	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B 1.1	D, H	protein	122	Xenopus laevis	P02281 (AlphaFold model)
DNA (145-mer)	I	DNA	145	Homo sapiens
DNA (145-mer)	J	DNA	145	Homo sapiens
N-lysine methyltransferase KMT5A	K	protein	221	Homo sapiens	Q9NQR1

Sequence of entity 1 (A, E), FASTA

>7XPX_1 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>7XPX_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRXVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>7XPX_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>7XPX_4 Histone H2B 1.1 (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Sequence of entity 5 (I), FASTA

>7XPX_5 DNA (145-MER) (chains I)
ATCACAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGGAATCCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTGTGAT

Sequence of entity 6 (J), FASTA

>7XPX_6 DNA (145-MER) (chains J)
ATCACAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGGATTCCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTGTGAT

Sequence of entity 7 (K), FASTA

>7XPX_7 N-lysine methyltransferase KMT5A (chains K)
MGSSHHHHHHSSENLYFQGHMAKQALKKPIKGKQAPRKKAQGKTQQNRKLTDFYPVRRSS
RKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIE
ITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQTKLHD
IDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH

Ligands and cofactors

ID	Name	Formula	Copies
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1

Primary citation

Structural basis of nucleosomal H4K20 methylation by methyltransferase SET8. Shi, L., Huang, L., Long, H. et al. FASEB J (2022) 36:e22338-e22338. DOI 10.1096/fj.202101821R · PubMed

Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome

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