3S8P: Histone-lysine N-methyltransferase SUV420H1

Name: PDB 3S8P: Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1 In Complex With S-Adenosyl-L-Methionine
Published: 2011-07-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1 In Complex With S-Adenosyl-L-Methionine. Determined by X-ray diffraction at 1.85 Å resolution. Released 6 Jul 2011.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,042
Mol. weight: 64.69 kDa
Ligands: SAM, ZN
Released: 6 Jul 2011

Explore 3S8P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3S8P contains 31 α-helices and 24 β-strands across 2 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: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	74-84	11
α-helix	85-89	5
α-helix	90-93	4
α-helix	134-147	14
α-helix	150-157	8
α-helix	161-167	7
α-helix	172-187	16
α-helix	191-193	3
β-strand	195-200	6	1
β-strand	209-214	6	1
β-strand	218	1	2
β-strand	223-234	12	3
α-helix	235	1
α-helix	236-242	7
β-strand	252-255	4	3
β-strand	260-265	6	3
α-helix	267-270	4
α-helix	271	1
β-strand	272-273	2	4
β-strand	279-285	7	3
β-strand	288-293	6	3
β-strand	297	1	2
α-helix	301	1
β-strand	302	1	1
α-helix	303	1
β-strand	304-305	2	4
α-helix	314-316	3
α-helix	322-327	6
α-helix	330-332	3

Chain B: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	74-88	15
α-helix	90-93	4
α-helix	133-147	15
α-helix	150-158	9
α-helix	163-167	5
α-helix	172-187	16
β-strand	195-200	6	5
β-strand	209-214	6	5
β-strand	218	1	6
β-strand	223-234	12	7
α-helix	236-242	7
β-strand	252-255	4	7
β-strand	260-265	6	7
α-helix	267-270	4
α-helix	271	1
β-strand	272-273	2	8
β-strand	279-285	7	7
β-strand	288-293	6	7
β-strand	297	1	6
α-helix	301	1
β-strand	302	1	5
α-helix	303	1
β-strand	304-305	2	8
α-helix	314-316	3
α-helix	322-327	6
α-helix	330-332	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SUV420H1	A, B	protein	273	Homo sapiens	Q4FZB7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3S8P_1 Histone-lysine N-methyltransferase SUV420H1 (chains A, B)
QSRYVPSSGMSAKELCENDDLATSLVLDPYLGFQTHKMNTSAFPSRSSRHFSKSDSFSHN
NPVRFRPIKGRQEELKEVIERFKKDEHLEKAFKCLTSGEWARHYFLNKNKMQEKLFKEHV
FIYLRMFATDSGFEILPCNRYSSEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEENML
LRHGENDFSVMYSTRKNCAQLWLGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPGEE
ISCYYGDGFFGENNEFCECYTCERRGTGAFKSR

Ligands and cofactors

ID	Name	Formula	Copies
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	2
ZN	Zinc ion	Zn	2

Primary citation

Crystal structures of the human histone H4K20 methyltransferases SUV420H1 and SUV420H2. Wu, H., Siarheyeva, A., Zeng, H. et al. FEBS Lett (2013) 587:3859-3868. PubMed

Other PDB entries of the same protein (UniProt Q4FZB7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
8T9F 2.6 Å, Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
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

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