1O9S: PDB entry 1O9S

Name: PDB 1O9S: Crystal structure of a ternary complex of the human histone methyltransferase SET7/9
Published: 2003-02-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of a ternary complex of the human histone methyltransferase SET7/9. Determined by X-ray diffraction at 1.75 Å resolution. Released 6 Feb 2003.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 4,767
Mol. weight: 61.07 kDa
Ligands: SAH
Released: 6 Feb 2003

Explore 1O9S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1O9S contains 17 α-helices and 44 β-strands across 4 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: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	118-122	5	1
β-strand	128-132	5	1
β-strand	141-147	7	1
β-strand	153-160	8	1
β-strand	163-176	14	1
β-strand	179-184	6	1
α-helix	185	1
β-strand	190-191	2	1
α-helix	210-215	6
β-strand	216-220	5	2
β-strand	228-232	5	2
β-strand	236	1	3
β-strand	241-245	5	4
β-strand	248-250	3	5
α-helix	252-256	5
α-helix	260-262	3
β-strand	267-268	2	5
β-strand	274-276	3	5
α-helix	292-294	3
α-helix	295	1
β-strand	296-297	2	4
β-strand	303-310	8	4
β-strand	314-321	8	4
β-strand	325	1	3
α-helix	329	1
β-strand	330-331	2	2
β-strand	332-333	2	4
β-strand	338	1	6
β-strand	348	1	6
α-helix	351-361	11

Chain B: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	118-122	5	7
β-strand	128-132	5	7
α-helix	133-134	2
β-strand	141-147	7	7
β-strand	153-160	8	7
β-strand	163-176	14	7
β-strand	179-184	6	7
α-helix	185	1
β-strand	191	1	7
α-helix	210-215	6
β-strand	216-220	5	8
β-strand	228-232	5	8
β-strand	236	1	9
β-strand	241-245	5	10
β-strand	248-251	4	11
α-helix	252-256	5
β-strand	267-268	2	11
β-strand	273-276	4	11
α-helix	292-294	3
α-helix	295	1
β-strand	296-297	2	10
β-strand	303-310	8	10
β-strand	314-321	8	10
β-strand	325	1	9
α-helix	329	1
β-strand	330-331	2	8
β-strand	332-333	2	10
α-helix	351-362	12

Chain K: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	5
α-helix	6-8	3

Chain L: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase, H3 lysine-4 specific	A, B	protein	259	HOMO SAPIENS	Q8WTS6 (AlphaFold model)
Gene fragment for histone H3	K, L	protein	10	HOMO SAPIENS	P68431 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1O9S_1 HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFIC (chains A, B)
GQYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEG
KLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAG
EGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKY
CASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGKSGP
EAPEWYQVELKAFQATQQK

Sequence of entity 2 (K, L), FASTA

>1O9S_2 GENE FRAGMENT FOR HISTONE H3 (chains K, L)
ARTKQTARKY

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2

Primary citation

Structure and Catalytic Mechanism of the Human Histone Methyltransferase Set7/9. Xiao, B., Jing, C., Wilson, J.R. et al. Nature (2003) 421:652. DOI 10.1038/NATURE01378 · PubMed

Other PDB entries of the same protein (UniProt Q8WTS6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2F69 1.3 Å, Ternary complex of SET7/9 bound to AdoHcy and a TAF10 peptide
3M58 1.4 Å, SET7/9 Y245A in complex with TAF10-K189me1 peptide and AdoHcy
3CBP 1.42 Å, Set7/9-ER-Sinefungin complex
3M55 1.55 Å, SET7/9 Y305F in complex with TAF10-K189me1 peptide and AdoHcy
5EG2 1.55 Å, SET7/9 N265A in complex with AdoHcy and TAF10 peptide
4J7F 1.59 Å, SET7/9Y335pAF in complex with TAF10 peptide and AdoHcy
3M54 1.6 Å, SET7/9 Y305F in complex with TAF10 peptide and AdoHcy
4J8O 1.63 Å, SET7/9 in complex with TAF10K189A peptide and AdoHcy
3CBO 1.65 Å, SET7/9-ER-AdoHcy complex
3M56 1.65 Å, SET7/9 Y305F in complex with TAF10-K189me2 peptide and AdoHcy
3CBM 1.69 Å, SET7/9-ER-AdoMet complex
3OS5 1.69 Å, SET7/9-Dnmt1 K142me1 complex

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