› 4u9w

X-ray diffraction
2.49Å resolution

Crystal Structure of NatD bound to H4/H2A peptide and CoA

Released:
DOI: 10.2210/pdb4u9w/pdb
PDB entry 4u9w coloured by chain, front view.
PDB entry 4u9w coloured by chain, side view.
PDB entry 4u9w coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The molecular basis for histone H4- and H2A-specific amino-terminal acetylation by NatD.
Magin RS, Liszczak GP, Marmorstein R
Structure 23 332-41 (2015)
PMID: 25619998

Function and Biology Details

Reaction catalysed: 
Acetyl-CoA + an N-terminal-L-seryl-[histone H2A] = an N-terminal-N(alpha)-acetyl-L-seryl-[histone H2A] + CoA
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158683 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
N-alpha-acetyltransferase 40 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 207 amino acids
Theoretical weight: 23.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q86UY6 (Residues: 17-220; Coverage: 86%)
Gene names: NAA40, NAT11, PATT1
Sequence domains: Acetyltransferase (GNAT) family
Histone H4 Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 6 amino acids
Theoretical weight: 504 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62805 (Residues: 2-6; Coverage: 5%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4

Ligands and Environments


Cofactor: Ligand COA 4 x COA
2 bound ligands:
Ligand NA 4 x NA
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21
Unit cell:
a: 52.901Å b: 93.288Å c: 100.329Å
α: 90° β: 96.69° γ: 90°
R-values:
R R work R free
0.178 0.176 0.223
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

Spotlight on protein N-terminal acetylation.
Ree et al. (2018)
8 more

9 mentions without citation

Structures and Strategies of Anti-CRISPR-Mediated Immune Suppression.
Wiegand et al. (2020)
8 more