› 7c9o

X-ray diffraction
2.55Å resolution

Crystal structure of DNA-bound CCT/NF-YB/YC complex (HD1CCT/GHD8/OsNF-YC2)

Released:
DOI: 10.2210/pdb7c9o/pdb
PDB entry 7c9o coloured by chain, front view.
PDB entry 7c9o coloured by chain, side view.
PDB entry 7c9o coloured by chain, top view.
Source organism: Oryza sativa Japonica Group
Primary publication:
Structural Insight into DNA Recognition by CCT/NF-YB/YC Complexes in Plant Photoperiodic Flowering.
Shen C, Liu H, Guan Z, Yan J, Zheng T, Yan W, Wu C, Zhang Q, Yin P, Xing Y
Plant Cell 32 3469-3484 (2020)
PMID: 32843433

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-107831 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (5 distinct):
Zinc finger protein HD1 Chain: A
Molecule details ›
Chain: A
Length: 67 amino acids
Theoretical weight: 8.08 KDa
Source organism: Oryza sativa Japonica Group
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9FDX8 (Residues: 311-375; Coverage: 17%)
Gene names: HD1, LOC_Os06g16370, Os06g0275000, P0038C05.23, P0676F10.34, SE1
Sequence domains: CCT motif
Nuclear transcription factor Y subunit B-11 Chain: B
Molecule details ›
Chain: B
Length: 95 amino acids
Theoretical weight: 10.85 KDa
Source organism: Oryza sativa Japonica Group
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q0J7P4 (Residues: 54-147; Coverage: 32%)
Gene names: DTH8, GHD8, HAP3H, HD5, LOC_Os08g07740, NFYB11, Os08g0174500
Sequence domains: Histone-like transcription factor (CBF/NF-Y) and archaeal histone
Nuclear transcription factor Y subunit C-2 Chain: C
Molecule details ›
Chain: C
Length: 104 amino acids
Theoretical weight: 11.91 KDa
Source organism: Oryza sativa Japonica Group
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A6BLW4 (Residues: 55-156; Coverage: 42%)
Gene names: HAP5C, LOC_Os03g14669, NFYC2, Os03g0251350
Sequence domains: Core histone H2A/H2B/H3/H4
DNA (25-MER) Chain: D
Molecule details ›
Chain: D
Length: 25 nucleotides
Theoretical weight: 7.53 KDa
DNA (25-MER) Chain: E
Molecule details ›
Chain: E
Length: 25 nucleotides
Theoretical weight: 7.83 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P3221
Unit cell:
a: 136.08Å b: 136.08Å c: 62.96Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.201 0.2 0.226
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

Rice functional genomics: decades' efforts and roads ahead.
Chen et al. (2022)
6 more