› 5fug

X-ray diffraction
2.7Å resolution

Crystal structure of a human YL1-H2A.Z-H2B complex

Released:
DOI: 10.2210/pdb5fug/pdb
PDB entry 5fug coloured by chain, front view.
PDB entry 5fug coloured by chain, side view.
PDB entry 5fug coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis and specificity of H2A.Z-H2B recognition and deposition by the histone chaperone YL1.
Latrick CM, Marek M, Ouararhni K, Papin C, Stoll I, Ignatyeva M, Obri A, Ennifar E, Dimitrov S, Romier C, Hamiche A
Nat Struct Mol Biol 23 309-16 (2016)
PMID: 26974126

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-139298 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Histone H2A.Z Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 110 amino acids
Theoretical weight: 11.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0C0S5 (Residues: 19-128; Coverage: 86%)
Gene names: H2AFZ, H2AZ, H2AZ1
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B type 1-J Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 96 amino acids
Theoretical weight: 10.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P06899 (Residues: 31-126; Coverage: 76%)
Gene names: H2BC11, H2BFR, HIST1H2BJ
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Vacuolar protein sorting-associated protein 72 homolog Chains: C, F, I, L
Molecule details ›
Chains: C, F, I, L
Length: 68 amino acids
Theoretical weight: 7.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q15906 (Residues: 6-69; Coverage: 18%)
Gene names: TCFL1, VPS72, YL1

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P21
Unit cell:
a: 36.12Å b: 150.68Å c: 92.61Å
α: 90° β: 91.47° γ: 90°
R-values:
R R work R free
0.182 0.177 0.243
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Fly Fishing for Histones: Catch and Release by Histone Chaperone Intrinsically Disordered Regions and Acidic Stretches.
Warren et al. (2017)
4 more

3 mentions without citation

Histone chaperone networks shaping chromatin function.
Hammond et al. (2017)
2 more