We've built a new version of this page with an interactive 3D viewer. Try it out in beta and help us improve:

› 8xjv

Electron Microscopy
3.6Å resolution

Structural basis for the linker histone H5-nucleosome binding and chromatin compaction

Released:
DOI: 10.2210/pdb8xjv/pdb
PDB entry 8xjv coloured by chain, front view.
PDB entry 8xjv coloured by chain, side view.
PDB entry 8xjv coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for linker histone H5-nucleosome binding and chromatin fiber compaction.
Li W, Hu J, Song F, Yu J, Peng X, Zhang S, Wang L, Hu M, Liu JC, Wei Y, Xiao X, Li Y, Li D, Wang H, Zhou BR, Dai L, Mou Z, Zhou M, Zhang H, Zhou Z, Zhang H, Bai Y, Zhou JQ, Li W, Li G, Zhu P
Cell Res (2024)
PMID: 39103524
Related structures: EMD-38407

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 110-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-275692 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H2A Chains: A, Ae, B, C, D, E, F, G, H, I, K, L, aj, ak, al, am, an, ao, ap, aq, ar, as, at, au
Molecule details ›
Chains: A, Ae, B, C, D, E, F, G, H, I, K, L, aj, ak, al, am, an, ao, ap, aq, ar, as, at, au
Length: 130 amino acids
Theoretical weight: 14.11 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6AZJ8 (Residues: 1-130; Coverage: 100%)
Gene names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
Sequence domains:
Histone H2B 1.1 Chains: Aa, Ab, Ac, Ad, Af, Ag, At, J, M, N, O, P, Q, R, S, T, U, V, W, av, aw, ax, ay, az
Molecule details ›
Chains: Aa, Ab, Ac, Ad, Af, Ag, At, J, M, N, O, P, Q, R, S, T, U, V, W, av, aw, ax, ay, az
Length: 123 amino acids
Theoretical weight: 13.64 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 H3 Chains: X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u
Molecule details ›
Chains: X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A310TTQ1 (Residues: 1-136; Coverage: 100%)
Gene names: LOC108703785, LOC121398065, LOC121398067
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, CD, a2, a3, a4, a5, a6, a7, a8, a9, v, w, x, y, z
Molecule details ›
Chains: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, CD, a2, a3, a4, a5, a6, a7, a8, a9, v, w, x, y, z
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H5 Chains: Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap, Aq, Ar, As
Molecule details ›
Chains: Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap, Aq, Ar, As
Length: 196 amino acids
Theoretical weight: 21.63 KDa
Source organism: Gallus gallus
Expression system: Escherichia coli
UniProt:
  • Canonical: P02259 (Residues: 1-190; Coverage: 100%)
Sequence domains: linker histone H1 and H5 family
DNA Chain: Au
Molecule details ›
Chain: Au
Length: 2124 nucleotides
Theoretical weight: 651.87 KDa
DNA Chain: Av
Molecule details ›
Chain: Av
Length: 2124 nucleotides
Theoretical weight: 660.63 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-38407
Expression system: Escherichia coli

Quick links