6LS6: YEATS domain of AF9

Crystal Structure of YEATS domain of AF9 in complex with H3K9bz peptide. Determined by X-ray diffraction at 2.2 Å resolution. Released 18 Nov 2020.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,479
Mol. weight: 35.27 kDa
Released: 18 Nov 2020

Explore 6LS6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6LS6 contains 10 α-helices and 24 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: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	9-22	14	1
β-strand	33-40	8	1
α-helix	42-44	3
α-helix	47-49	3
β-strand	51-57	7	2
β-strand	66-69	4	2
β-strand	74-80	7	1
β-strand	83	1	3
β-strand	84-92	9	2
β-strand	100-107	8	2
β-strand	110	1	4
α-helix	111	1
α-helix	115-116	2
β-strand	117-128	12	1
α-helix	132-140	9

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	9-22	14	5
β-strand	33-40	8	5
α-helix	42-44	3
α-helix	47-49	3
β-strand	51-57	7	6
β-strand	66-69	4	6
β-strand	74-80	7	5
β-strand	83	1	7
β-strand	84-92	9	6
β-strand	100-107	8	6
β-strand	110	1	8
α-helix	111	1
α-helix	115-116	2
β-strand	117-128	12	5
α-helix	132-139	8

Chains C and D: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	8
β-strand	8	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein AF-9	A, B	protein	141	Homo sapiens	P42568 (AlphaFold model)
2	C, D	protein	8	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6LS6_1 Protein AF-9 (chains A, B)
GSHMASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHE
SFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRKVRFDYDLFLHLEGHPPVNHL
RCEKLTFNNPTEDFRRKLLKA

Sequence of entity 2 (C, D), FASTA

>6LS6_2 2 (chains C, D)
TKQTARKS

Primary citation

Histone benzoylation serves as an epigenetic mark for DPF and YEATS family proteins. Ren, X., Zhou, Y., Xue, Z. et al. Nucleic Acids Res (2021) 49:114-126. DOI 10.1093/nar/gkaa1130 · PubMed

Other PDB entries of the same protein (UniProt P42568 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PJ7 1.26 Å, MLLT3 in complex with compound PFI-6
7VKG 1.83 Å, Crystal structure of AF9 YEATS domain in complex with Compound 10
5YYF 1.9 Å, Crystal structure of AF9 YEATS domain in complex with a peptide inhibitor…
6MIL 1.93 Å, Crystal structure of AF9 YEATS domain in complex with histone H3K9bu
7EIC 1.95 Å, Crystal structure of AF9 YEATS domain in complex with H4K5acK8ac peptide
7EID 2.0 Å, Crystal structure of AF9 YEATS domain in complex with H4K8acK12ac peptide
8TLX 2.1 Å, Crystal structure of MBP and AF9 AHD fusion protein 3AQA in complex with peptidomimetic…
9ARR 2.1 Å, Crystal structure of AF9 YEATS domain in complex with dicrotonylated at K1007 and K1014…
8TLW 2.11 Å, Crystal structure of MBP and AF9 AHD fusion protein 3AQA in complex with peptidomimetic…
7VKH 2.25 Å, Crystal structure of AF9 YEATS domain in complex with hit 2
4TMP 2.3 Å, Crystal structure of AF9 YEATS bound to H3K9ac peptide
9ARO 2.3 Å, Crystal structure of AF9 YEATS domain in complex with acetylated at K1007 MOZ

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