› 5wcu

X-ray diffraction
5.53Å resolution

Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5

Released:
DOI: 10.2210/pdb5wcu/pdb
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PDB entry 5wcu coloured by chain, front view.
PDB entry 5wcu coloured by chain, side view.
PDB entry 5wcu coloured by chain, top view.
Source organisms:
Primary publication:
Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures.
Zhou BR, Jiang J, Ghirlando R, Norouzi D, Sathish Yadav KN, Feng H, Wang R, Zhang P, Zhurkin V, Bai Y
J Mol Biol 430 3093-3110 (2018)
PMID: 29959925

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119342 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H3 Chains: A, E, K, O
Molecule details ›
Chains: A, E, K, O
Length: 98 amino acids
Theoretical weight: 11.49 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: P02299 (Residues: 39-136; Coverage: 72%)
Gene names: CG31613, CG33803, CG33806, CG33809, CG33812, CG33815, CG33818, CG33821, CG33824, CG33827, CG33830, CG33833, CG33836, CG33839, CG33842, CG33845, CG33848, CG33851, CG33854, CG33857, CG33860, CG33863, CG33866, His3, His3:CG31613, His3:CG33803, His3:CG33806, His3:CG33809, His3:CG33812, His3:CG33815, His3:CG33818, His3:CG33821, His3:CG33824, His3:CG33827, His3:CG33830, His3:CG33833, His3:CG33836, His3:CG33839, His3:CG33842, His3:CG33845, His3:CG33848, His3:CG33851, His3:CG33854, His3:CG33857, His3:CG33860, His3:CG33863, His3:CG33866
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F, L, P
Molecule details ›
Chains: B, F, L, P
Length: 82 amino acids
Theoretical weight: 9.28 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: P84040 (Residues: 22-103; Coverage: 80%)
Gene names: CG31611, CG3379, CG33869, CG33871, CG33873, CG33875, CG33877, CG33879, CG33881, CG33883, CG33885, CG33887, CG33889, CG33891, CG33893, CG33895, CG33897, CG33899, CG33901, CG33903, CG33905, CG33907, CG33909, H4, H4r, His4, His4:CG31611, His4:CG33869, His4:CG33871, His4:CG33873, His4:CG33875, His4:CG33877, His4:CG33879, His4:CG33881, His4:CG33883, His4:CG33885, His4:CG33887, His4:CG33889, His4:CG33891, His4:CG33893, His4:CG33895, His4:CG33897, His4:CG33899, His4:CG33901, His4:CG33903, His4:CG33905, His4:CG33907, His4:CG33909, His4r
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A Chains: C, G, M, Q
Histone H2B Chains: D, H, N, R
Histone H5 Chains: U, V
DNA (167-MER) Chains: I, S
DNA (167-MER) Chains: J, T

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P1
Unit cell:
a: 65.926Å b: 108.543Å c: 180.77Å
α: 100.79° β: 90.08° γ: 89.94°
R-values:
R R work R free
0.195 0.189 0.238
Expression system: Escherichia coli

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Citations

3 review citations

Principles of nucleosome recognition by chromatin factors and enzymes.
McGinty et al. (2021)
2 more

7 mentions without citation

Structures of monomeric and dimeric PRC2:EZH1 reveal flexible modules involved in chromatin compaction.
Grau et al. (2021)
6 more

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