› 5av6

X-ray diffraction
2.2Å resolution

human nucleosome core particle

Released:
DOI: 10.2210/pdb5av6/pdb
Model geometry
Fit model/data
PDB entry 5av6 coloured by chain, front view.
PDB entry 5av6 coloured by chain, side view.
PDB entry 5av6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation.
Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S
OpenAccess logo Sci Rep 5 17204 (2015)
PMID: 26607036

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-118403 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Histone H3.1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 139 amino acids
Theoretical weight: 15.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P68431 (Residues: 1-136; Coverage: 100%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 104 amino acids
Theoretical weight: 11.45 KDa
Source organism: Homo sapiens
Expression system: CELL-FREE SYNTHESIS
UniProt:
  • Canonical: P62805 (Residues: 1-103; Coverage: 100%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A type 1-B/E Chains: C, G
Histone H2B type 1-J Chains: D, H
DNA (147-MER) Chain: I
DNA (147-MER) Chain: J

Ligands and Environments

1 bound ligand:
Ligand MN 14 x MN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: P212121
Unit cell:
a: 106.385Å b: 110.042Å c: 182.302Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.201 0.229
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • CELL-FREE SYNTHESIS

Quick links

Citations

5 review citations

Recent Development of Genetic Code Expansion for Posttranslational Modification Studies.
Chen et al. (2018)
4 more

4 mentions without citation

Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment.
Zhou et al. (2019)
3 more

PDB-REDO

The sliders below show the change in model quality between original PDB entry and the PDB-REDO entry

Model Geometry
 
 
Data not available
DNA/RNA Geometry
 
 
Data not available
Fit model/data
 
 
Data not available
PDB-REDO