6MIL: AF9 YEATS domain

Crystal structure of AF9 YEATS domain in complex with histone H3K9bu. Determined by X-ray diffraction at 1.93 Å resolution. Released 14 Nov 2018.

Method: X-ray diffraction
Resolution: 1.93 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,814
Mol. weight: 37.72 kDa
Ligands: MLI
Released: 14 Nov 2018

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

Secondary structure: helices and β-sheets

6MIL 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	4-19	16	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

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

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

Chain C: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-19	17	1
β-strand	30-37	8	1
α-helix	44-46	3
β-strand	48-54	7	5
β-strand	63-66	4	5
β-strand	71-77	7	1
β-strand	80	1	6
β-strand	81-89	9	5
α-helix	95	1
β-strand	97-104	8	5
β-strand	107	1	7
α-helix	108	1
α-helix	112-113	2
β-strand	114-125	12	1
α-helix	129-137	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein AF-9	A, C	protein	141	Homo sapiens	P42568 (AlphaFold model)
Histone H3K9bu	B, D	protein	19	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6MIL_1 Protein AF-9 (chains A, C)
GSHMASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHE
SFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRKVRFDYDLFLHLEGHPPVNHL
RCEKLTFNNPTEDFRRKLLKA

Sequence of entity 2 (B, D), FASTA

>6MIL_2 Histone H3K9bu (chains B, D)
ARTKQTARXSTGGKAPRKQ

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	1

Water and common crystallization additives (PEG) are not listed.

Primary citation

Structural insights into the pi-pi-pi stacking mechanism and DNA-binding activity of the YEATS domain. Klein, B.J., Vann, K.R., Andrews, F.H. et al. Nat Commun (2018) 9:4574-4574. DOI 10.1038/s41467-018-07072-6 · 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…
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
9ARO 2.3 Å, Crystal structure of AF9 YEATS domain in complex with acetylated at K1007 MOZ

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