› 5g49

X-ray diffraction
2.3Å resolution

Crystal structure of the Arabodopsis thaliana histone-fold dimer L1L NF-YC3

Released:
DOI: 10.2210/pdb5g49/pdb
PDB entry 5g49 coloured by chain, front view.
PDB entry 5g49 coloured by chain, side view.
PDB entry 5g49 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Crystal Structure of the Arabidopsis thaliana L1L/NF-YC3 Histone-fold Dimer Reveals Specificities of the LEC1 Family of NF-Y Subunits in Plants.
Gnesutta N, Saad D, Chaves-Sanjuan A, Mantovani R, Nardini M
Mol Plant 10 645-648 (2017)
PMID: 27871811

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183068 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Nuclear transcription factor Y subunit B-6 Chain: A
Molecule details ›
Chain: A
Length: 97 amino acids
Theoretical weight: 11.48 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q84W66 (Residues: 55-147; Coverage: 40%)
Gene names: At5g47670, L1L, MNJ7.26, NFYB6
Sequence domains: Histone-like transcription factor (CBF/NF-Y) and archaeal histone
Structure domains: Histone, subunit A
Nuclear transcription factor Y subunit C-3 Chain: B
Molecule details ›
Chain: B
Length: 95 amino acids
Theoretical weight: 11.13 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9ZVL3 (Residues: 55-148; Coverage: 43%)
Gene names: At1g54830, F14C21.41, NFYC3, T22H22.22
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A

Ligands and Environments

2 bound ligands:
Ligand CA 1 x CA
Ligand ACT 3 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: C2221
Unit cell:
a: 68.344Å b: 81.691Å c: 95.998Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.164 0.162 0.2
Expression system: Escherichia coli

Quick links

Citations

7 review citations

The Arabidopsis thaliana Nuclear Factor Y Transcription Factors.
Zhao et al. (2016)
6 more

1 mention without citation

Isolation, characterization and expression analysis of stress responsive plant nuclear transcriptional factor subunit (NF-YB2) from commercial Saccharum hybrid and wild relative Erianthus arundinaceus.
Peter et al. (2020)