› 6r2v

X-ray diffraction
2.5Å resolution

Arabidopsis NF-Y/CCAAT-box complex

Released:
DOI: 10.2210/pdb6r2v/pdb
PDB entry 6r2v coloured by chain, front view.
PDB entry 6r2v coloured by chain, side view.
PDB entry 6r2v coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Structural determinants for NF-Y subunit organization and NF-Y/DNA association in plants.
Chaves-Sanjuan A, Gnesutta N, Gobbini A, Martignago D, Bernardini A, Fornara F, Mantovani R, Nardini M
Plant J 105 49-61 (2021)
PMID: 33098724

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-120523 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (5 distinct):
Nuclear transcription factor Y subunit A-6 Chain: A
Molecule details ›
Chain: A
Length: 75 amino acids
Theoretical weight: 8.87 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9LVJ7 (Residues: 170-237, 238-241; Coverage: 23%)
Gene names: At3g14020, MDC16.15, NFYA6
Sequence domains: CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B
Nuclear transcription factor Y subunit B-2 Chain: B
Molecule details ›
Chain: B
Length: 97 amino acids
Theoretical weight: 11.16 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9FGJ3 (Residues: 24-116; Coverage: 49%)
Gene names: At5g47640, HAP3B, MNJ7.23, NFYB2
Sequence domains: Histone-like transcription factor (CBF/NF-Y) and archaeal histone
Nuclear transcription factor Y subunit C-3 Chain: C
Molecule details ›
Chain: C
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
FT (-5kb) CCAAT-box 5' Chain: I
Molecule details ›
Chain: I
Length: 25 nucleotides
Theoretical weight: 7.55 KDa
FT (-5kb) CCAAT-box 3' Chain: J
Molecule details ›
Chain: J
Length: 25 nucleotides
Theoretical weight: 7.8 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: 53.446Å b: 85.525Å c: 130.305Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.2 0.247
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Plant transcription factors - being in the right place with the right company.
Strader et al. (2022)
7 more