9IM4: AF9 YEATS domain F28R mutant

Crystal Structure of AF9 YEATS domain F28R mutant in complex with histone H3K9la. Determined by X-ray diffraction at 2.79 Å resolution. Released 9 Jul 2025.

Method: X-ray diffraction
Resolution: 2.79 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,474
Mol. weight: 39.46 kDa
Released: 9 Jul 2025

Explore 9IM4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IM4 contains 10 α-helices and 26 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	6-18	13	1
β-strand	30-37	8	1
α-helix	39-41	3
α-helix	44-46	3
β-strand	48-54	7	2
β-strand	63-66	4	2
β-strand	71-77	7	1
β-strand	80	1	3
β-strand	81-89	9	2
β-strand	97-104	8	2
β-strand	107	1	4
α-helix	108	1
α-helix	112-113	2
β-strand	114-125	12	1
α-helix	129-137	9

Chain B: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-19	14	5
β-strand	30-37	8	5
β-strand	38	1	6
α-helix	39-41	3
β-strand	42	1	6
α-helix	44-46	3
β-strand	48-54	7	7
β-strand	63-66	4	7
β-strand	71-77	7	5
β-strand	80	1	8
β-strand	81-89	9	7
β-strand	97-104	8	7
β-strand	107	1	9
α-helix	108	1
α-helix	112-113	2
β-strand	114-125	12	5
α-helix	129-135	7

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

Element	Residues	Length	Sheet
β-strand	5	1	9
β-strand	8	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein AF-9	A, B	protein	158	Homo sapiens	P42568 (AlphaFold model)
Histone H3.3C	C, P	protein	10	Homo sapiens	Q6NXT2 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9IM4_1 Protein AF-9 (chains A, B)
MGSSHHHHHHSSGLVPRGSHMASSCAVQVKLELGHRAQVRKKPTVEGRTHDWMVFVRGPE
HSNIQHFVEKVVFHLHESFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRKVRF
DYDLFLHLEGHPPVNHLRCEKLTFNNPTEDFRRKLLKA

Sequence of entity 2 (C, P), FASTA

>9IM4_2 Histone H3.3C (chains C, P)
ARTKQTARXS

Primary citation

AF9-KLF2 gene regulatory circuit links histone lactylation to metabolic reprogramming and breast cancer progression. Ma, H., Yuan, M., Yang, C. et al. Cell Rep (2026) 45:117429-117429. DOI 10.1016/j.celrep.2026.117429 · 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…
6LS6 2.2 Å, Crystal Structure of YEATS domain of AF9 in complex with H3K9bz peptide
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

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