› 3c1b

X-ray diffraction
2.2Å resolution

The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure

Released:
DOI: 10.2210/pdb3c1b/pdb
PDB entry 3c1b coloured by chain, front view.
PDB entry 3c1b coloured by chain, side view.
PDB entry 3c1b coloured by chain, top view.
Source organisms:
Primary publication:
The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure.
Lu X, Simon MD, Chodaparambil JV, Hansen JC, Shokat KM, Luger K
Nat Struct Mol Biol 15 1122-4 (2008)
PMID: 18794842

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116115 (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (5 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.3 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 102 amino acids
Theoretical weight: 11.32 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
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: 129 amino acids
Theoretical weight: 14.01 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B Chains: D, H
Molecule details ›
Chains: D, H
Length: 125 amino acids
Theoretical weight: 13.81 KDa
Source organism: Xenopus tropicalis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q28D68 (Residues: 2-126; Coverage: 99%)
Gene names: LOC100495396, LOC101731959, LOC101733171, LOC108648861, LOC108648863, LOC108648864, LOC108648866, LOC116407582, LOC116407584, LOC116407585, LOC116407586, LOC116407587, LOC116407588, LOC116407589, LOC116407590, LOC116407592, TGas058p09.1-001, XENTR_v90029327mg, XENTR_v90029353mg, hist2h2bf
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Palindromic 146bp Human Alpha satellite DNA Chains: I, J
Molecule details ›
Chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa

Ligands and Environments

No bound ligands
1 modified residue:
Ligand ML3 2 x ML3

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P212121
Unit cell:
a: 105.67Å b: 109.83Å c: 181.03Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.24 0.24 0.27
Expression system: Escherichia coli

Quick links

Citations

62 review citations

Histone core modifications regulating nucleosome structure and dynamics.
Tessarz et al. (2014)
61 more

10 mentions without citation

Histones: at the crossroads of peptide and protein chemistry.
Müller et al. (2015)
9 more