› 7pex

Electron Microscopy
5.1Å resolution

Nucleosome 2 of the 4x177 nucleosome array containing H1

Released:
DOI: 10.2210/pdb7pex/pdb
PDB entry 7pex coloured by chain, front view.
PDB entry 7pex coloured by chain, side view.
PDB entry 7pex coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory.
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
OpenAccess logo Nat Struct Mol Biol 29 493-501 (2022)
PMID: 35581345
Related structures: EMD-13360

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-121794 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H3.2 Chains: a, e
Molecule details ›
Chains: a, e
Length: 136 amino acids
Theoretical weight: 15.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q71DI3 (Residues: 1-136; Coverage: 100%)
Gene names: H3C13, H3C14, H3C15, H3F2, H3FM, HIST2H3A, HIST2H3C, HIST2H3D
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: b, f
Molecule details ›
Chains: b, f
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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
Histone H2A type 1-B/E Chains: c, g
Molecule details ›
Chains: c, g
Length: 147 amino acids
Theoretical weight: 16.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04908 (Residues: 1-130; Coverage: 100%)
Gene names: H2AC4, H2AC8, H2AFA, H2AFM, HIST1H2AB, HIST1H2AE
Sequence domains:
Histone H2B type 1-K Chains: d, h
Molecule details ›
Chains: d, h
Length: 126 amino acids
Theoretical weight: 13.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60814 (Residues: 1-126; Coverage: 100%)
Gene names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H1.4 Chain: u
Molecule details ›
Chain: u
Length: 218 amino acids
Theoretical weight: 21.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P10412 (Residues: 2-219; Coverage: 100%)
Gene names: H1-4, H1F4, HIST1H1E
Sequence domains: linker histone H1 and H5 family
DNA (177-MER) Chain: J
Molecule details ›
Chain: J
Length: 177 nucleotides
Theoretical weight: 55.01 KDa
DNA (177-MER) Chain: I
Molecule details ›
Chain: I
Length: 177 nucleotides
Theoretical weight: 54.28 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.1Å
Relevant EMDB volumes: EMD-13360
Expression system: Escherichia coli

Quick links

Citations

2 review citations

The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response.
Belousova et al. (2022)
1 more

1 mention without citation

Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory.
Dombrowski et al. (2022)