2F69: Ternary complex of SET7/9

Ternary complex of SET7/9 bound to AdoHcy and a TAF10 peptide. Determined by X-ray diffraction at 1.3 Å resolution. Released 17 Jan 2006.

Method: X-ray diffraction
Resolution: 1.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,498
Mol. weight: 30.7 kDa
Ligands: SAH
Released: 17 Jan 2006

Explore 2F69 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2F69 contains 8 α-helices and 21 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: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	119-122	4	1
β-strand	128-131	4	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	210-213	4
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
α-helix	351-363	13

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	189	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase, H3 lysine-4 specific SET7	A	protein	261	Homo sapiens	Q8WTS6 (AlphaFold model)
TAF10 peptide, Acetyl-Ser-Lys-Ser-Mlz-Asp-Arg-Lys-Tyr-Thr-Leu	B	protein	11		Q12962 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2F69_1 Histone-lysine N-methyltransferase, H3 lysine-4 specific SET7 (chains A)
GAMGYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMI
EGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISS
AGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVS
KYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGKS
GPEAPEWYQVELKAFQATQQK

Sequence of entity 2 (B), FASTA

>2F69_2 TAF10 peptide, Acetyl-Ser-Lys-Ser-Mlz-Asp-Arg-Lys-Tyr-Thr-Leu (chains B)
XSKSKDRKYTL

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1

Primary citation

Structural basis for the methylation site specificity of SET7/9. Couture, J.-F., Collazo, E., Hauk, G. et al. Nat Struct Mol Biol (2006) 13:140-146. DOI 10.1038/nsmb1045 · PubMed

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

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
5YLT 1.69 Å, Crystal structure of SET7/9 in complex with a cyproheptadine derivative

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