3F9Z: Histone-lysine N-methyltransferase SETD8

Name: PDB 3F9Z: Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy
Published: 2008-11-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy. Determined by X-ray diffraction at 1.6 Å resolution. Released 25 Nov 2008.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 8
Atoms: 6,115
Mol. weight: 81.77 kDa
Ligands: SAH
Released: 25 Nov 2008

Explore 3F9Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3F9Z contains 31 α-helices and 56 β-strands across 8 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: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	195-212	18
β-strand	218-223	6	1
β-strand	227-232	6	1
α-helix	235	1
β-strand	236	1	2
α-helix	237	1
β-strand	241-244	4	3
β-strand	248-251	4	4
α-helix	252-262	11
β-strand	272-277	6	4
β-strand	280-285	6	4
α-helix	294-296	3
β-strand	298-299	2	3
β-strand	305-312	8	3
β-strand	315-322	8	3
β-strand	326	1	2
α-helix	330	1
β-strand	331	1	1
α-helix	332	1
β-strand	333-334	2	3
α-helix	341-346	6
α-helix	348-351	4

Chain B: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	195-212	18
β-strand	218-223	6	5
β-strand	227-232	6	5
β-strand	236	1	6
β-strand	241-245	5	7
β-strand	248-251	4	8
α-helix	252-262	11
β-strand	272-277	6	8
β-strand	280-285	6	8
α-helix	294-296	3
β-strand	298-299	2	9
β-strand	305-312	8	7
β-strand	315-322	8	7
β-strand	326	1	6
α-helix	330	1
β-strand	331	1	5
α-helix	332	1
β-strand	333-334	2	9
α-helix	341-346	6
α-helix	348-351	4

Chain C: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	195-212	18
β-strand	218-223	6	10
β-strand	227-232	6	10
β-strand	236	1	11
β-strand	241-245	5	12
β-strand	248-251	4	13
α-helix	252-263	12
β-strand	272-277	6	13
β-strand	280-285	6	13
α-helix	294-296	3
β-strand	298-299	2	14
β-strand	305-312	8	12
β-strand	315-322	8	12
β-strand	326	1	11
α-helix	330	1
β-strand	331	1	10
α-helix	332	1
β-strand	333-334	2	14
α-helix	341-346	6
α-helix	348-351	4

Chain D: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	195-212	18
β-strand	218-223	6	15
β-strand	227-232	6	15
β-strand	236	1	16
β-strand	241-245	5	17
β-strand	248-251	4	18
α-helix	252-262	11
β-strand	272-277	6	18
β-strand	280-285	6	18
α-helix	294-296	3
α-helix	297	1
β-strand	298-299	2	17
β-strand	305-312	8	17
β-strand	315-322	8	17
β-strand	326	1	16
α-helix	330	1
β-strand	331	1	15
α-helix	332	1
β-strand	333-334	2	17
α-helix	341-346	6
α-helix	348-351	4

Chain E: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	20-22	3	8

Chains F and H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	20-21	2	4

Chain G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	21	1	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SETD8	A, B, C, D	protein	166	Homo sapiens	Q9NQR1 (AlphaFold model)
Histone H4	E, F, G, H	protein	10		P62805 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3F9Z_1 Histone-lysine N-methyltransferase SETD8 (chains A, B, C, D)
GAMGSRKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEFH
GDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQ
TKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH

Sequence of entity 2 (E, F, G, H), FASTA

>3F9Z_2 Histone H4 (chains E, F, G, H)
AKRHRKVLRD

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	4

Primary citation

Structural origins for the product specificity of SET domain protein methyltransferases. Couture, J.F., Dirk, L.M., Brunzelle, J.S. et al. Proc Natl Acad Sci U S A (2008) 105:20659-20664. DOI 10.1073/pnas.0806712105 · PubMed

Other PDB entries of the same protein (UniProt Q9NQR1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3F9X 1.25 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
5TEG 1.3 Å, Crystal structure of hSETD8 in complex with histone H4K20 norleucine mutant peptide and…
1ZKK 1.45 Å, Crystal structure of hSET8 in ternary complex with H4 peptide (16-24) and AdoHcy
2BQZ 1.5 Å, Crystal structure of a ternary complex of the human histone methyltransferase Pr-SET7…
3F9Y 1.5 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
3F9W 1.6 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
5W1Y 1.7 Å, SETD8 in complex with a covalent inhibitor
5TH7 1.95 Å, Complex of SETD8 with MS453
4IJ8 2.0 Å, Crystal structure of the complex of SETD8 with SAM
5V2N 2.0 Å, Crystal Structure of APO Human SETD8
9CR7 2.05 Å, Structure of human SETD8 in complex with covalent inhibitor AM2928
5T5G 2.1 Å, human SETD8 in complex with MS2177

Browse structure collections

About this viewer

MolViewer shows 3F9Z 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.