7C9O

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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.

(2020) Plant Cell 32: 3469-3484

  • DOI: https://doi.org/10.1105/tpc.20.00067
  • Primary Citation of Related Structures:  
    7C9O, 7C9P

  • PubMed Abstract: 

    CONSTANS, CONSTANS-LIKE, and TIMING OF CAB EXPRESSION1 (CCT) domain-containing proteins are a large family unique to plants. They transcriptionally regulate photoperiodic flowering, circadian rhythms, vernalization, and other related processes. Through their CCT domains, CONSTANS and HEADING DATE1 (HD1) coordinate with the NUCLEAR FACTOR Y (NF-Y) B/C dimer to specifically target a conserved 'CCACA' motif within the promoters of their target genes. However, the mechanism underlying DNA recognition by the CCT domain remains unclear. Here we determined the crystal structures of the rice ( Oryza sativa ) NF-YB/YC dimer and the florigen gene Heading date 3a ( Hd3a )-bound HD1 CCT /NF-YB/YC trimer with resolutions of 2.0 Å and 2.55 Å, respectively. The CCT domain of HD1 displays an elongated structure containing two α-helices and two loops, tethering Hd3a to the NF-YB/YC dimer. Helix α2 and loop 2 are anchored into the minor groove of the 'CCACA' motif, which determines the specific base recognition. Our structures reveal the interaction mechanism among the CCT domain, NF-YB/YC dimer, and the target DNA. These results not only provide insight into the network between the CCT proteins and NF-Y subunits, but also offer potential approaches for improving productivity and global adaptability of crops by manipulating florigen expression.


  • Organizational Affiliation

    National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein HD167Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: HD1SE1Os06g0275000LOC_Os06g16370P0038C05.23P0676F10.34
UniProt
Find proteins for Q9FDX8 (Oryza sativa subsp. japonica)
Explore Q9FDX8 
Go to UniProtKB:  Q9FDX8
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UniProt GroupQ9FDX8
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear transcription factor Y subunit B-1195Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: HD5DTH8GHD8HAP3HNFYB11Os08g0174500LOC_Os08g07740
UniProt
Find proteins for Q0J7P4 (Oryza sativa subsp. japonica)
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Go to UniProtKB:  Q0J7P4
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UniProt GroupQ0J7P4
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear transcription factor Y subunit C-2104Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: NFYC2HAP5COs03g0251350LOC_Os03g14669
UniProt
Find proteins for A6BLW4 (Oryza sativa subsp. japonica)
Explore A6BLW4 
Go to UniProtKB:  A6BLW4
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UniProt GroupA6BLW4
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (25-MER)25Oryza sativa
Sequence Annotations
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (25-MER)25Oryza sativa
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.08α = 90
b = 136.08β = 90
c = 62.96γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2020-11-18
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description