› 5zba

X-ray diffraction
3.5Å resolution

Crystal structure of Rtt109-Asf1-H3-H4-CoA complex

Released:
DOI: 10.2210/pdb5zba/pdb
PDB entry 5zba coloured by chain, front view.
PDB entry 5zba coloured by chain, side view.
PDB entry 5zba coloured by chain, top view.
Source organisms:
Primary publication:
Multisite Substrate Recognition in Asf1-Dependent Acetylation of Histone H3 K56 by Rtt109.
Zhang L, Serra-Cardona A, Zhou H, Wang M, Yang N, Zhang Z, Xu RM
Cell 174 818-830.e11 (2018)
PMID: 30057113

Function and Biology Details

Reaction catalysed: 
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-135458 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
histone acetyltransferase Chain: A
Molecule details ›
Chain: A
Length: 544 amino acids
Theoretical weight: 59.68 KDa
Source organism: Aspergillus fumigatus Af293
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q4WUS9 (Residues: 1-543; Coverage: 100%)
Gene name: AFUA_5G09540
Sequence domains: Histone acetylation protein
Histone chaperone asf1 Chain: B
Molecule details ›
Chain: B
Length: 188 amino acids
Theoretical weight: 21.1 KDa
Source organism: Aspergillus fumigatus Af293
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q4WXX5 (Residues: 1-154; Coverage: 55%)
Gene names: AFUA_3G11030, asf1
Sequence domains: ASF1 like histone chaperone
Structure domains: Histone chaperone ASF1-like
Histone H3 Chain: C
Molecule details ›
Chain: C
Length: 136 amino acids
Theoretical weight: 15.39 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P61830 (Residues: 1-136; Coverage: 100%)
Gene names: HHT1, HHT2, N2749, SIN2, YBR010W, YBR0201, YNL031C
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chain: D
Molecule details ›
Chain: D
Length: 103 amino acids
Theoretical weight: 11.4 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P02309 (Residues: 1-103; Coverage: 100%)
Gene names: HHF1, HHF2, N2752, YBR009C, YBR0122, YNL030W
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A

Ligands and Environments


Cofactor: Ligand COA 1 x COA
1 bound ligand:
Ligand IOD 37 x IOD
1 modified residue:
Ligand ALY 1 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P6522
Unit cell:
a: 111.903Å b: 111.903Å c: 332.715Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.245 0.243 0.294
Expression system: Escherichia coli BL21

Quick links

Citations

7 review citations

The replisome guides nucleosome assembly during DNA replication.
Zhang et al. (2020)
6 more

3 mentions without citation

Multisite Substrate Recognition in Asf1-Dependent Acetylation of Histone H3 K56 by Rtt109.
Zhang et al. (2018)
2 more