› 4awl

X-ray diffraction
3.08Å resolution

The NF-Y transcription factor is structurally and functionally a sequence specific histone

Released:
DOI: 10.2210/pdb4awl/pdb
PDB entry 4awl coloured by chain, front view.
PDB entry 4awl coloured by chain, side view.
PDB entry 4awl coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Sequence-specific transcription factor NF-Y displays histone-like DNA binding and H2B-like ubiquitination.
Nardini M, Gnesutta N, Donati G, Gatta R, Forni C, Fossati A, Vonrhein C, Moras D, Romier C, Bolognesi M, Mantovani R
Cell 152 132-43 (2013)
PMID: 23332751

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117225 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (5 distinct):
Nuclear transcription factor Y subunit alpha Chain: A
Molecule details ›
Chain: A
Length: 78 amino acids
Theoretical weight: 9.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P23511 (Residues: 262-332; Coverage: 21%)
Gene name: NFYA
Sequence domains: CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Nuclear transcription factor Y subunit beta Chain: B
Molecule details ›
Chain: B
Length: 94 amino acids
Theoretical weight: 10.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P25208 (Residues: 51-143; Coverage: 45%)
Gene names: HAP3, NFYB
Sequence domains: Histone-like transcription factor (CBF/NF-Y) and archaeal histone
Structure domains: Histone, subunit A
Nuclear transcription factor Y subunit gamma Chain: C
Molecule details ›
Chain: C
Length: 94 amino acids
Theoretical weight: 11.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13952 (Residues: 27-120; Coverage: 21%)
Gene name: NFYC
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
HSP70 PROMOTER FRAGMENT Chain: I
Molecule details ›
Chain: I
Length: 25 nucleotides
Theoretical weight: 7.62 KDa
HSP70 PROMOTER FRAGMENT Chain: J
Molecule details ›
Chain: J
Length: 25 nucleotides
Theoretical weight: 7.74 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P212121
Unit cell:
a: 54.7Å b: 62.56Å c: 139.68Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.191 0.25
Expression system: Escherichia coli

Quick links

Citations

20 review citations

Interplay between Metabolism and Epigenetics: A Nuclear Adaptation to Environmental Changes.
Etchegaray et al. (2016)
19 more

12 mentions without citation

Pioneer Factors in Animals and Plants-Colonizing Chromatin for Gene Regulation.
Lai et al. (2018)
11 more