› 5e5a

X-ray diffraction
2.81Å resolution

Crystal structure of the chromatin-tethering domain of Human cytomegalovirus IE1 protein bound to the nucleosome core particle

Released:
DOI: 10.2210/pdb5e5a/pdb
PDB entry 5e5a coloured by chain, front view.
PDB entry 5e5a coloured by chain, side view.
PDB entry 5e5a coloured by chain, top view.
Source organisms:
Primary publication:
Human cytomegalovirus IE1 protein alters the higher-order chromatin structure by targeting the acidic patch of the nucleosome.
Fang Q, Chen P, Wang M, Fang J, Yang N, Li G, Xu RM
Elife 5 (2016)
PMID: 26812545

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-118611 (preferred)
Entry contents:
5 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (6 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 1-136; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 130 amino acids
Theoretical weight: 14.11 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 123 amino acids
Theoretical weight: 13.66 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Immediate early protein IE1 Chain: K
Molecule details ›
Chain: K
Length: 16 amino acids
Theoretical weight: 1.7 KDa
Source organism: Human herpesvirus 5 strain Towne
Expression system: Not provided
UniProt:
  • Canonical: P03169 (Residues: 476-491; Coverage: 3%)
Gene name: UL123
DNA (146-MER) Chains: I, J
Molecule details ›
Chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa

Ligands and Environments

1 bound ligand:
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P212121
Unit cell:
a: 106.7Å b: 109.474Å c: 181.976Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.196 0.242
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

Nucleosome structure and dynamics are coming of age.
Zhou et al. (2019)
7 more

6 mentions without citation

Principles of nucleosome recognition by chromatin factors and enzymes.
McGinty et al. (2021)
5 more