› 1m19

X-ray diffraction
2.3Å resolution

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

Released:
DOI: 10.2210/pdb1m19/pdb
PDB entry 1m19 coloured by chain, front view.
PDB entry 1m19 coloured by chain, side view.
PDB entry 1m19 coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands.
Suto RK, Edayathumangalam RS, White CL, Melander C, Gottesfeld JM, Dervan PB, Luger K
J Mol Biol 326 371-80 (2003)
PMID: 12559907

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-114162 (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (5 distinct):
Histone H3.3C Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.32 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02302 (Residues: 2-136; Coverage: 99%)
Gene names: h3-5, h3f3c
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: 11.26 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: 13.96 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 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 125 amino acids
Theoretical weight: 13.85 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 2-126; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Palindromic 146 Base Pair DNA Fragment Chains: I, J
Molecule details ›
Chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa

Ligands and Environments

6 bound ligands:
Ligand MN 11 x MN
Ligand IMT 5 x IMT
Ligand PYB 35 x PYB
Ligand ABU 5 x ABU
Ligand BAL 5 x BAL
Ligand DIB 5 x DIB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P212121
Unit cell:
a: 107.045Å b: 109.662Å c: 183.018Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.214 0.253
Expression system: Escherichia coli

Quick links

Citations

27 review citations

New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?
Luger et al. (2012)
26 more

7 mentions without citation

Histone structure and nucleosome stability.
Mariño-Ramírez et al. (2005)
6 more