7CVQ

crystal structure of Arabidopsis CO CCT domain in complex with NF-YB2/YC3 and FT CORE1 DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the multivalent binding of the Arabidopsis FLOWERING LOCUS T promoter by the CO-NF-Y master transcription factor complex.

Lv, X.Zeng, X.Hu, H.Chen, L.Zhang, F.Liu, R.Liu, Y.Zhou, X.Wang, C.Wu, Z.Kim, C.He, Y.Du, J.

(2021) Plant Cell 33: 1182-1195

  • DOI: https://doi.org/10.1093/plcell/koab016
  • Primary Citation of Related Structures:  
    7CVO, 7CVQ

  • PubMed Abstract: 

    Flowering plants sense various environmental and endogenous signals to trigger the floral transition and start the reproductive growth cycle. CONSTANS (CO) is a master transcription factor in the photoperiod floral pathway that integrates upstream signals and activates the florigen gene FLOWERING LOCUS T (FT). Here, we performed comprehensive structural and biochemical analyses to study the molecular mechanism underlying the regulation of FT by CO in Arabidopsis thaliana. We show that the four previously characterized cis-elements in the FT promoter proximal region, CORE1, CORE2, P1, and P2, are all direct CO binding sites. Structural analysis of CO in complex with NUCLEAR FACTOR-YB/YC (NF-YB/YC) and the CORE2 or CORE1 elements revealed the molecular basis for the specific recognition of the shared TGTG motifs. Biochemical analysis suggested that CO might form a homomultimeric assembly via its N-terminal B-Box domain and simultaneously occupy multiple cis-elements within the FT promoter. We suggest that this multivalent binding gives the CO-NF-Y complex high affinity and specificity for FT promoter binding. Overall, our data provide a detailed molecular model for the regulation of FT by the master transcription factor complex CO-NF-Y during the floral transition.


  • Organizational Affiliation

    National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chimera of Nuclear transcription factor Y subunit C-3 and Zinc finger protein CONSTANSA,
E [auth F],
F [auth K],
G [auth P]
174Arabidopsis thalianaMutation(s): 0 
Gene Names: NFYC3At1g54830F14C21.41T22H22.22COAt5g15840F14F8_220
UniProt
Find proteins for Q39057 (Arabidopsis thaliana)
Explore Q39057 
Go to UniProtKB:  Q39057
Find proteins for Q9ZVL3 (Arabidopsis thaliana)
Explore Q9ZVL3 
Go to UniProtKB:  Q9ZVL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ39057Q9ZVL3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear transcription factor Y subunit B-2B,
H [auth G],
I [auth L],
J [auth Q]
97Arabidopsis thalianaMutation(s): 0 
Gene Names: NFYB2HAP3BAt5g47640MNJ7.23
UniProt
Find proteins for Q9FGJ3 (Arabidopsis thaliana)
Explore Q9FGJ3 
Go to UniProtKB:  Q9FGJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FGJ3
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
FT CORE1 DNA forward strandC [auth D],
K [auth I],
L [auth N],
M [auth T]
25Arabidopsis thaliana
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
FT CORE1 DNA reverse strandD [auth E],
N [auth J],
O,
P [auth U]
25Arabidopsis thaliana
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.244α = 90
b = 65.273β = 91.17
c = 138.284γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2021-06-16 
  • Deposition Author(s): Lv, X., Du, J.

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description