7F4E: Hst2

Crystal structure of Hst2 in complex with H3K9bz peptide. Determined by X-ray diffraction at 1.78 Å resolution. Released 16 Mar 2022.

Method: X-ray diffraction
Resolution: 1.78 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 2
Atoms: 2,528
Mol. weight: 33.73 kDa
Ligands: ZN
Released: 16 Mar 2022

Explore 7F4E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7F4E contains 20 α-helices and 17 β-strands across 2 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: 18 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	9-21	13
β-strand	27-31	5	1
α-helix	33-39	7
α-helix	53-57	5
α-helix	65-67	3
β-strand	68	1	2
α-helix	69-74	6
α-helix	77-86	10
α-helix	92-94	3
α-helix	95-105	11
β-strand	109-114	6	1
α-helix	120-123	4
α-helix	128-130	3
β-strand	131-133	3	1
β-strand	136-143	8	3
β-strand	149-150	2	3
α-helix	153-159	7
β-strand	169	1	4
β-strand	176	1	4
β-strand	177-181	5	3
β-strand	184	1	2
β-strand	187	1	5
α-helix	188-189	2
α-helix	190-203	14
β-strand	218-222	5	1
β-strand	229	1	6
α-helix	231-233	3
α-helix	234-237	4
β-strand	243-247	5	1
α-helix	254-257	4
β-strand	264-266	3	1
α-helix	270-281	12
α-helix	284-291	8

Chain C: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7	1
β-strand	8	1	5
α-helix	9	1
β-strand	10	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacetylase HST2	A	protein	287	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53686 (AlphaFold model)
Histone H3	C	protein	10	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P61830 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7F4E_1 NAD-dependent protein deacetylase HST2 (chains A)
TEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVF
DVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNIDTLERQAGVK
DDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGED
LPDSFSETWLNDSEWLREKITTSGKHPQQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLC
NLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTAQ

Sequence of entity 2 (C), FASTA

>7F4E_2 Histone H3 (chains C)
QTARKSTGGK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Global profiling of regulatory elements in the histone benzoylation pathway. Wang, D., Yan, F., Wu, P. et al. Nat Commun (2022) 13:1369-1369. DOI 10.1038/s41467-022-29057-2 · PubMed

Other PDB entries of the same protein (UniProt P53686 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1Q1A 1.5 Å, Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP…
1SZD 1.5 Å, Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent…
1SZC 1.75 Å, Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent…
7F51 1.98 Å, Crystal structure of Hst2 in complex with 2'-O-Benzoyl ADP Ribose
2OD2 2.0 Å, Crystal Structure of yHst2 I117F mutant bound to carba-NAD+ and an acetylated H4 peptide
2OD7 2.0 Å, Crystal Structure of yHst2 bound to the intermediate analogue ADP-HPD, and and aceylated…
2QQF 2.0 Å, Hst2 bound to ADP-HPD and Acetylated histone H4
2OD9 2.05 Å, Structural Basis for Nicotinamide Inhibition and Base Exchange in Sir2 Enzymes
2QQG 2.05 Å, Hst2 bound to ADP-HPD, acetyllated histone H4 and nicotinamide
1Q14 2.5 Å, Structure and autoregulation of the yeast Hst2 homolog of Sir2
1Q17 2.7 Å, Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP…

Browse structure collections

About this viewer

MolViewer shows 7F4E directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.