› 3lel

X-ray diffraction
2.95Å resolution

Structural Insight into the Sequence-Dependence of Nucleosome Positioning

Released:
DOI: 10.2210/pdb3lel/pdb
PDB 3lel coloured by chain and viewed from the front.
PDB 3lel coloured by chain and viewed from the side.
PDB 3lel coloured by chain and viewed from the top.
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:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (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, XELAEV_18003602mg, h2ac14, 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

8 review citations

Contributions of Sequence to the Higher-Order Structures of DNA.
Todolli et al. (2017)
7 more

5 mentions without citation

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