› › Structure analysis

Nucleosome core particle containing 145 bp of DNA

X-ray diffraction
2.65Å resolution
PDB entry 2nzd coloured by chain, front view.
PDB entry 2nzd coloured by chain, side view.
PDB entry 2nzd coloured by chain, top view.
Source organism: Xenopus laevis
Assembly composition:
hetero decamer (preferred)
Entry contents: 4 distinct polypeptide molecules
2 distinct DNA molecules

Quick links

Assemblies

Assembly 1 (preferred)
Download    3D Visualisation
Assembly Name: Nucleosome, Histone and DNA
hide full assembly name
Multimeric state: hetero decamer
Accessible surface area: 74082.73 Å2
Buried surface area: 58322.53 Å2
Dissociation area: 7,142.35 Å2
Dissociation energy (ΔGdiss): 98.81 kcal/mol
Dissociation entropy (TΔSdiss): 28.71 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-115693

Macromolecules

Histone H3.2
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%)
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
CATH: Histone, subunit A
SCOP: Nucleosome core histones
Histone H3.2 in PDB entry 2nzd, assembly 1, front view.
Histone H3.2 in PDB entry 2nzd, assembly 1, side view.
Histone H3.2 in PDB entry 2nzd, assembly 1, top view.
Molecule details ›

Search similar proteins

Histone H4
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%)
Pfam: Centromere kinetochore component CENP-T histone fold
InterPro:
CATH: Histone, subunit A
SCOP: Nucleosome core histones
Histone H4 in PDB entry 2nzd, assembly 1, front view.
Histone H4 in PDB entry 2nzd, assembly 1, side view.
Histone H4 in PDB entry 2nzd, assembly 1, top view.
Molecule details ›

Search similar proteins

Histone H2A type 1
Chains: C, G
Length: 119 amino acids
Theoretical weight: 12.94 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-120; Coverage: 92%)
Pfam:
InterPro:
CATH: Histone, subunit A
SCOP: Nucleosome core histones
Histone H2A type 1 in PDB entry 2nzd, assembly 1, front view.
Histone H2A type 1 in PDB entry 2nzd, assembly 1, side view.
Histone H2A type 1 in PDB entry 2nzd, assembly 1, top view.
Molecule details ›

Search similar proteins

Histone H2B 1.1
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%)
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
CATH: Histone, subunit A
Histone H2B 1.1 in PDB entry 2nzd, assembly 1, front view.
Histone H2B 1.1 in PDB entry 2nzd, assembly 1, side view.
Histone H2B 1.1 in PDB entry 2nzd, assembly 1, top view.
Molecule details ›

Search similar proteins

DNA chain I
Name: DNA (145-MER)
Representative chains: I
Length: 145 nucleotides
Theoretical weight: 44.75 KDa
DNA (145-MER) in PDB entry 2nzd, assembly 1, front view.
DNA (145-MER) in PDB entry 2nzd, assembly 1, side view.
DNA (145-MER) in PDB entry 2nzd, assembly 1, top view.
Molecule details ›

Search similar DNA

DNA chain J
Name: DNA (145-MER)
Representative chains: J
Length: 145 nucleotides
Theoretical weight: 44.74 KDa
DNA (145-MER) in PDB entry 2nzd, assembly 1, front view.
DNA (145-MER) in PDB entry 2nzd, assembly 1, side view.
DNA (145-MER) in PDB entry 2nzd, assembly 1, top view.
Molecule details ›

Search similar DNA

Quick links