5HJD: AF9 YEATS

AF9 YEATS in complex with histone H3 Crotonylation at K18. Determined by X-ray diffraction at 2.81 Å resolution. Released 20 Apr 2016.

Method: X-ray diffraction
Resolution: 2.81 Å
Organism: Homo sapiens
Chains: 16
Atoms: 9,775
Mol. weight: 141.31 kDa
Ligands: CU
Released: 20 Apr 2016

Explore 5HJD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HJD contains 29 α-helices and 88 β-strands across 16 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: 3 helices, 9 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	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
α-helix	112-113	2
β-strand	114-125	12	1
α-helix	129-137	9

Chains B, D, F, H, I, J, L and M: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	17	1	3

Chain C: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	5-19	15	1
β-strand	30-37	8	1
α-helix	39-41	3
α-helix	44-46	3
β-strand	48-54	7	4
β-strand	63-66	4	4
β-strand	71-77	7	1
β-strand	80	1	5
β-strand	81-89	9	4
β-strand	97-104	8	4
α-helix	112-113	2
β-strand	114-125	12	1
α-helix	129-137	9

Chain E: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	6
β-strand	6-19	14	7
β-strand	30-37	8	7
α-helix	38	1
α-helix	44-46	3
β-strand	48-54	7	8
β-strand	63-66	4	8
β-strand	71-77	7	7
β-strand	80	1	9
β-strand	81-89	9	8
β-strand	97-104	8	8
α-helix	107-108	2
β-strand	114-125	12	7
α-helix	129-137	9

Chain G: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	7
β-strand	6-19	14	6
β-strand	30-37	8	6
α-helix	39-41	3
α-helix	44-46	3
β-strand	48-54	7	10
β-strand	63-66	4	10
β-strand	71-74	4	6
β-strand	77	1	6
β-strand	80	1	11
β-strand	81-89	9	10
β-strand	97-104	8	10
α-helix	112-113	2
β-strand	114-125	12	6
α-helix	129-136	8

Chain K: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	12
β-strand	6-19	14	13
β-strand	30-37	8	13
α-helix	44-46	3
β-strand	48-54	7	14
β-strand	63-66	4	14
β-strand	71-77	7	13
β-strand	80	1	15
β-strand	81-89	9	14
β-strand	97-104	8	14
α-helix	112-113	2
β-strand	114-125	12	13
α-helix	129-136	8

Chain N: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	13
β-strand	6-19	14	12
β-strand	30-37	8	12
α-helix	39-41	3
α-helix	44-46	3
β-strand	48-54	7	16
β-strand	63-66	4	16
β-strand	71-74	4	12
β-strand	77	1	12
β-strand	80	1	17
β-strand	81-89	9	16
β-strand	97-104	8	16
α-helix	112-113	2
β-strand	114-125	12	12
α-helix	129-137	9

Chain Q: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	18
β-strand	6-19	14	19
β-strand	30-37	8	19
α-helix	44-46	3
β-strand	48-54	7	20
β-strand	63-66	4	20
β-strand	71-77	7	19
β-strand	80	1	21
β-strand	81-89	9	20
β-strand	97-104	8	20
α-helix	112-113	2
β-strand	114-125	12	19
α-helix	129-137	9

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein AF-9	A, C, E, G, K, N, Q, T	protein	140	Homo sapiens	P42568 (AlphaFold model)
peptide of Histone H3.1	B, D, F, H, I, J, L, M	protein	7	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, K, N, Q, T), FASTA

>5HJD_1 Protein AF-9 (chains A, C, E, G, K, N, Q, T)
SHMASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHES
FPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRKVRFDYDLFLHLEGHPPVNHLR
CEKLTFNNPTEDFRRKLLKA

Sequence of entity 2 (B, D, F, H, I, J, L, M), FASTA

>5HJD_2 peptide of Histone H3.1 (chains B, D, F, H, I, J, L, M)
KAPRXQL

Ligands and cofactors

ID	Name	Formula	Copies
CU	Copper (II) ion	Cu	4

Water and common crystallization additives (SO4) are not listed.

Primary citation

Molecular Coupling of Histone Crotonylation and Active Transcription by AF9 YEATS Domain. Li, Y.Y., Sabari, B.R., Panchenko, T. et al. Mol Cell (2016) 62:181-193. DOI 10.1016/j.molcel.2016.03.028 · 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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