7VSP | pdb_00007vsp

Crystal strcuture of the tandem B-Box domains of COL2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7VSP

This is version 1.2 of the entry. See complete history

Literature

Molecular basis of CONSTANS oligomerization in FLOWERING LOCUS T activation.

Zeng, X.Lv, X.Liu, R.He, H.Liang, S.Chen, L.Zhang, F.Chen, L.He, Y.Du, J.

(2022) J Integr Plant Biol 64: 731-740

  • DOI: https://doi.org/10.1111/jipb.13223
  • Primary Citation Related Structures: 
    7VSP, 7VSQ

  • PubMed Abstract: 

    The transcription factor CONSTANS (CO) integrates day-length information to induce the expression of florigen FLOWERING LOCUS T (FT) in Arabidopsis. We recently reported that the C-terminal CCT domain of CO forms a complex with NUCLEAR FACTOR-YB/YC to recognize multiple cis-elements in the FT promoter, and the N-terminal tandem B-box domains form a homomultimeric assembly. However, the mechanism and biological function of CO multimerization remained unclear. Here, we report that CO takes on a head-to-tail oligomeric configuration via its B-boxes to mediate FT activation in long days. The crystal structure of B-boxes CO reveals a closely connected tandem B-box fold forming a continuous head-to-tail assembly through unique CDHH zinc fingers. Mutating the key residues involved in CO oligomerization resulted in a non-functional CO, as evidenced by the inability to rescue co mutants. By contrast, a transgene encoding a human p53-derived tetrameric peptide in place of the B-boxes CO rescued co mutant, emphasizing the essential role of B-boxes CO -mediated oligomerization. Furthermore, we found that the four TGTG-bearing cis-elements in FT proximal promoter are required for FT activation in long days. Our results suggest that CO forms a multimer to bind to the four TGTG motifs in the FT promoter to mediate FT activation.


  • Organizational Affiliation
    • Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.

Macromolecule Content 

  • Total Structure Weight: 40.23 kDa 
  • Atom Count: 2,134 
  • Modeled Residue Count: 271 
  • Deposited Residue Count: 363 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc finger protein CONSTANS-LIKE 2
A, B, C
121Arabidopsis thalianaMutation(s): 0 
Gene Names: COL2At3g02380F11A12.106F11A12.7F16B3.2
UniProt
Find proteins for Q96502 (Arabidopsis thaliana)
Explore Q96502 
Go to UniProtKB:  Q96502
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96502
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.934α = 90
b = 44.478β = 100.05
c = 99.765γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaJCYJ20200109110403829

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-03-30
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Database references, Structure summary