8T9H: Histone H3.2

Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. Determined by electron microscopy at 3.37 Å resolution. Released 13 Sept 2023.

Method: Electron microscopy
Resolution: 3.37 Å
Organisms: Xenopus laevis, Escherichia coli 'BL21-Gold(DE3)pLysS AG', Homo sapiens
Chains: 11
Atoms: 12,039
Mol. weight: 243.76 kDa
Released: 13 Sept 2023

Explore 8T9H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T9H contains 50 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: 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	121-130	10

Chain B: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	3
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	4
α-helix	50-75	26
β-strand	80-81	2	5
α-helix	83-92	10
β-strand	96-98	3	6

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	7
α-helix	46-72	27
β-strand	77-78	2	8
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	9

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	33-35	3
α-helix	38-48	11
β-strand	53-54	2	8
α-helix	56-83	28
β-strand	88-89	2	7
α-helix	91-101	11
α-helix	105-122	18

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	5
α-helix	86-113	28
β-strand	118-119	2	4
α-helix	121-130	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45-46	2	2
α-helix	50-76	27
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	96-98	3	9

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
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	6

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	40-49	10
β-strand	54-55	2	11
α-helix	57-84	28
β-strand	89-90	2	10
α-helix	92-102	11
α-helix	105-123	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 H3.2	A, E	protein	135	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	130	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B 1.1	D, H	protein	123	Xenopus laevis	P02281 (AlphaFold model)
DNA (146-mer)	I	DNA	146	Escherichia coli 'BL21-Gold(DE3)pLysS AG'
DNA (146-mer)	J	DNA	146	Escherichia coli 'BL21-Gold(DE3)pLysS AG'
Histone-lysine N-methyltransferase KMT5B	K	protein	394	Homo sapiens	Q4FZB7

Sequence of entity 1 (A, E), FASTA

>8T9H_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>8T9H_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRMVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>8T9H_3 Histone H2A (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>8T9H_4 Histone H2B 1.1 (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK

Sequence of entity 5 (I), FASTA

>8T9H_5 DNA (146-MER) (chains I)
TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGGATTCTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCGAT

Sequence of entity 6 (J), FASTA

>8T9H_6 DNA (146-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGAGAATCCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGA

Sequence of entity 7 (K), FASTA

>8T9H_7 Histone-lysine N-methyltransferase KMT5B (chains K)
GSKWLGESKNMVVNGRRNGGKLSNDHQQNQSKLQHTGKDTLKAGKNAVERRSNRCNGNSG
FEGQSRYVPSSGMSAKELCENDDLATSLVLDPYLGFQTHKMNTSAFPSRSSRHFSKSDSF
SHNNPVRFRPIKGRQEELKEVIERFKKDEHLEKAFKCLTSGEWARHYFLNKNKMQEKLFK
EHVFIYLRMFATDSGFEILPCNRYSSEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEE
NMLLRHGENDFSVMYSTRKNCAQLWLGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEP
GEEISCYYGDGFFGENNEFCECYTCERRGTGAFKSRVGLPAPAPVINSKYGLRETDKRLN
RLKKLGDSSKNSDSQSVSSNTDADTTQEKNNASK

Primary citation

Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. Abini-Agbomson, S., Gretarsson, K., Shih, R.M. et al. Mol Cell (2023) 83:2872-2883.e7. DOI 10.1016/j.molcel.2023.07.020 · 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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