› 3lel

X-ray diffraction
2.95Å resolution

Structural Insight into the Sequence-Dependence of Nucleosome Positioning

Released:
DOI: 10.2210/pdb3lel/pdb
PDB entry 3lel coloured by chain, front view.
PDB entry 3lel coloured by chain, side view.
PDB entry 3lel coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Structural insight into the sequence dependence of nucleosome positioning.
Wu B, Mohideen K, Vasudevan D, Davey CA
Structure 18 528-36 (2010)
PMID: 20399189

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116527 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Histone H3.2 Chains: A, E, K, O
Molecule details ›
Chains: A, E, K, O
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, L, P
Molecule details ›
Chains: B, F, L, P
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 Chains: C, G, M, Q
Molecule details ›
Chains: C, G, M, Q
Length: 128 amino acids
Theoretical weight: 13.91 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6AZJ8 (Residues: 2-130; Coverage: 99%)
Gene names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H, N, R
Molecule details ›
Chains: D, H, N, R
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
147-MER DNA Chains: I, S
Molecule details ›
Chains: I, S
Length: 147 nucleotides
Theoretical weight: 45.36 KDa
147-MER DNA Chains: J, T
Molecule details ›
Chains: J, T
Length: 147 nucleotides
Theoretical weight: 45.35 KDa

Ligands and Environments

1 bound ligand:
Ligand MN 34 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 106.747Å b: 178.508Å c: 110.412Å
α: 90° β: 102.78° γ: 90°
R-values:
R R work R free
0.231 0.229 0.3
Expression system: Escherichia coli

Quick links

Citations

9 review citations

On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease.
Cooper et al. (2011)
8 more

5 mentions without citation

Nucleosome structural studies.
Tan et al. (2011)
4 more