8T9F: Histone-lysine N-methyltransferase KMT5B

Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. Determined by electron microscopy at 2.6 Å resolution. Released 6 Sept 2023.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Homo sapiens, Escherichia coli 'BL21-Gold(DE3)pLysS AG', Xenopus laevis
Chains: 11
Atoms: 13,132
Mol. weight: 243.09 kDa
Ligands: SAM
Released: 6 Sept 2023

Explore 8T9F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T9F contains 52 α-helices and 32 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	8
α-helix	86-113	28
β-strand	118-119	2	9
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	31-40	10
β-strand	45-46	2	5
α-helix	50-75	26
β-strand	80-81	2	6
α-helix	83-92	10
β-strand	97-98	2	7

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-22	4
α-helix	29-38	10
β-strand	45-46	2	13
α-helix	48-75	28
β-strand	80-81	2	14
α-helix	83-92	10
α-helix	94-99	6
β-strand	103-104	2	10
α-helix	115-118	4

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	14
α-helix	56-83	28
β-strand	88-89	2	13
α-helix	91-101	11
α-helix	105-119	15
α-helix	120-124	5

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	6
α-helix	86-113	28
β-strand	118-119	2	5
α-helix	121-130	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	9
α-helix	50-75	26
β-strand	80-81	2	8
α-helix	83-93	11
β-strand	97-98	2	10

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-22	4
α-helix	29-38	10
β-strand	45-46	2	11
α-helix	48-75	28
β-strand	80-81	2	12
α-helix	83-92	10
α-helix	94-99	6
β-strand	103-104	2	7

Chain H: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	39-49	11
β-strand	54-55	2	12
α-helix	57-84	28
β-strand	89-90	2	11
α-helix	92-102	11
α-helix	106-120	15
α-helix	121-125	5

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-lysine N-methyltransferase KMT5B	K	protein	393	Homo sapiens	Q4FZB7 (AlphaFold model)
DNA (122-mer)	I	DNA	146	Escherichia coli 'BL21-Gold(DE3)pLysS AG'
DNA (122-mer)	J	DNA	146	Escherichia coli 'BL21-Gold(DE3)pLysS AG'
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H3.2	A, E	protein	135	Xenopus laevis	P84233 (AlphaFold model)
Histone H2A.Z	C, G	protein	128	Homo sapiens	P0C0S5 (AlphaFold model)
Histone H2B 1.1	D, H	protein	123	Xenopus laevis	P02281

Sequence of entity 1 (K), FASTA

>8T9F_1 Histone-lysine N-methyltransferase KMT5B (chains K)
MKWLGESKNMVVNGRRNGGKLSNDHQQNQSKLQHTGKDTLKAGKNAVERRSNRCNGNSGF
EGQSRYVPSSGMSAKELCENDDLATSLVLDPYLGFQTHKMNTSAFPSRSSRHFSKSDSFS
HNNPVRFRPIKGRQEELKEVIERFKKDEHLEKAFKCLTSGEWARHYFLNKNKMQEKLFKE
HVFIYLRMFATDSGFEILPCNRYSSEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEEN
MLLRHGENDFSVMYSTRKNCAQLWLGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPG
EEISCYYGDGFFGENNEFCECYTCERRGTGAFKSRVGLPAPAPVINSKYGLRETDKRLNR
LKKLGDSSKNSDSQSVSSNTDADTTQEKNNASK

Sequence of entity 2 (I), FASTA

>8T9F_2 DNA (122-MER) (chains I)
TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGGATTCTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCGAT

Sequence of entity 3 (J), FASTA

>8T9F_3 DNA (122-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGAGAATCCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGA

Sequence of entity 4 (B, F), FASTA

>8T9F_4 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRMVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (A, E), FASTA

>8T9F_5 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 6 (C, G), FASTA

>8T9F_6 Histone H2A.Z (chains C, G)
MAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILE
YLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIG
KKGQQKTV

Sequence of entity 7 (D, H), FASTA

>8T9F_7 Histone H2B 1.1 (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK

Ligands and cofactors

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

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 Q4FZB7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3S8P 1.85 Å, Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1…
8T68 1.9 Å, Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1…
5CPR 2.22 Å, The novel SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity
5WBV 2.3 Å, Crystal Structure of the SET Domain of Human SUV420H1 In Complex With Inhibitor
7YRD 3.2 Å, histone methyltransferase
8T9H 3.37 Å, Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
8JHG 3.58 Å, Native SUV420H1 bound to 167-bp nucleosome
8JHF 3.68 Å, Native SUV420H1 bound to 167-bp nucleosome
7YRG 4.2 Å, histone methyltransferase

Browse structure collections

About this viewer

MolViewer shows 8T9F directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.