5VNA: Human YEATS domain

Crystal structure of human YEATS domain. Determined by X-ray diffraction at 2.1 Å resolution. Released 5 Sept 2018.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,670
Mol. weight: 70.48 kDa
Ligands: NHE
Released: 5 Sept 2018

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

Secondary structure: helices and β-sheets

5VNA contains 13 α-helices and 34 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: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
β-strand	20-33	14	2
β-strand	45-53	9	2
α-helix	59-61	3
β-strand	63-69	7	3
β-strand	78-81	4	3
β-strand	86-92	7	2
β-strand	97-104	8	3
α-helix	110-111	2
β-strand	112-117	6	3
α-helix	122-123	2
α-helix	124-128	5
β-strand	134-145	12	2

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	22-33	12	4
β-strand	45-53	9	4
β-strand	63-69	7	5
β-strand	78-81	4	5
β-strand	86-92	7	4
β-strand	97-104	8	5
α-helix	110-111	2
β-strand	112-117	6	5
α-helix	118-119	2
α-helix	122-123	2
α-helix	124-128	5
β-strand	134-143	10	4

Chain C: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	21-33	13	6
β-strand	45-53	9	6
α-helix	59-61	3
β-strand	63-69	7	7
β-strand	78-81	4	7
β-strand	86-92	7	6
β-strand	97-104	8	7
α-helix	110-111	2
β-strand	112-117	6	7
β-strand	134-144	11	6

Chain D: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	22-38	17	8
β-strand	43-53	11	8
α-helix	59-61	3
β-strand	63-69	7	9
β-strand	78-81	4	9
β-strand	86-92	7	8
β-strand	95	1	1
β-strand	97-104	8	9
α-helix	110-111	2
β-strand	112-117	6	9
α-helix	124-129	6
β-strand	133-143	11	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
YEATS domain-containing protein 4	A, B, C, D	protein	148	Homo sapiens	O95619 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5VNA_1 YEATS domain-containing protein 4 (chains A, B, C, D)
MFKRMAEFGPDSGGRVKGVTIVKPIVYGNVARYFGKKREEDGHTHQWTVYVKPYRNEDMS
AYVKKIQFKLHESYGNPLRVVTKPPYEITETGWGEFEIIIKIFFIDPNERPVTLYHLLKL
FQSDTNAMLGKKTVVSEFYDEMIFQDPT

Ligands and cofactors

ID	Name	Formula	Copies
NHE	2-[N-cyclohexylamino]ethane sulfonic acid	C8 H17 N O3 S	1

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

Primary citation

GAS41 Recognizes Diacetylated Histone H3 through a Bivalent Binding Mode. Cho, H.J., Li, H., Linhares, B.M. et al. ACS Chem Biol (2018) 13:2739-2746. DOI 10.1021/acschembio.8b00674 · PubMed

Other PDB entries of the same protein (UniProt O95619 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8IJ0 1.52 Å, Crystal structure of GAS41 YEATS domain in complex with H3K9ac peptide
7EIF 1.58 Å, Crystal structure of GAS41 YEATS domain
5R68 1.64 Å, XChem group deposition -- Crystal Structure of human YEATS4 in complex with FM000199e
9X8S 1.7 Å, Crystal structure of the human GAS41 YEATS domain in complex with an acetylated YFV…
5R69 1.83 Å, XChem group deposition -- Crystal Structure of human YEATS4 in complex with XS038644e
8IIZ 2.1 Å, Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K27ac peptide
7JFY 2.1 Å, GAS41 YEATS domain in complex with 5
5XTZ 2.1 Å, Crystal structure of GAS41 YEATS bound to H3K27ac peptide
8IIY 2.15 Å, Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac peptide
8I60 2.3 Å, Crystal structure of GAS41 YEATS domain in complex with histone H3K27cr
9O4Y 2.3 Å, GAS41 YEATS domain in complex with DLG-1
5VNB 2.4 Å, YEATS in complex with histone H3

Browse structure collections

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