› 5nl0

X-ray diffraction
5.4Å resolution

Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1

Released:
DOI: 10.2210/pdb5nl0/pdb
PDB entry 5nl0 coloured by chain, front view.
PDB entry 5nl0 coloured by chain, side view.
PDB entry 5nl0 coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1.
Bednar J, Garcia-Saez I, Boopathi R, Cutter AR, Papai G, Reymer A, Syed SH, Lone IN, Tonchev O, Crucifix C, Menoni H, Papin C, Skoufias DA, Kurumizaka H, Lavery R, Hamiche A, Hayes JJ, Schultz P, Angelov D, Petosa C, Dimitrov S
Mol Cell 66 384-397.e8 (2017)
PMID: 28475873

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero undecamer (preferred)
hetero hexamer
Assembly name:
PDBe Complex ID:
PDB-CPX-119063 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H3.2 Chains: A, E, K
Molecule details ›
Chains: A, E, K
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
Histone H4 Chains: B, F, L
Molecule details ›
Chains: B, F, L
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
Histone H2A type 1 Chains: C, G, M
Molecule details ›
Chains: C, G, M
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Sequence domains:
Histone H2B 1.1 Chains: D, H, N
Molecule details ›
Chains: D, H, N
Length: 122 amino acids
Theoretical weight: 13.52 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
Histone H1.0-B Chain: Z
Molecule details ›
Chain: Z
Length: 196 amino acids
Theoretical weight: 21.13 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P22844 (Residues: 1-196; Coverage: 100%)
Gene name: h1-0-b
Sequence domains: linker histone H1 and H5 family
DNA (197-MER) Chains: I, S
Molecule details ›
Chains: I, S
Length: 197 nucleotides
Theoretical weight: 60.82 KDa
DNA (197-MER) Chains: J, T
Molecule details ›
Chains: J, T
Length: 197 nucleotides
Theoretical weight: 60.82 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: C2221
Unit cell:
a: 61.725Å b: 405.737Å c: 348.162Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.242 0.24 0.265
Expression system: Escherichia coli

Quick links

Citations

37 review citations

Emerging roles of linker histones in regulating chromatin structure and function.
Fyodorov et al. (2018)
36 more

32 mentions without citation

Histone Tail Conformations: A Fuzzy Affair with DNA.
Ghoneim et al. (2021)
31 more