6R0L

Histone fold domain of OsGhd8/NF-YC7 in I2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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.

(2021) Plant J 105: 49-61

  • DOI: https://doi.org/10.1111/tpj.15038
  • Primary Citation of Related Structures:  
    6R0L, 6R0M, 6R0N, 6R2V

  • PubMed Abstract: 

    NF-Y transcription factor comprises three subunits: NF-YA, NF-YB and NF-YC. NF-YB and NF-YC dimerize through their histone fold domain (HFD), which can bind DNA in a non-sequence-specific fashion while serving as a scaffold for NF-YA trimerization. Upon trimerization, NF-YA specifically recognizes the CCAAT box sequence on promoters and enhancers. In plants, each NF-Y subunit is encoded by several genes giving rise to hundreds of potential heterotrimeric combinations. In addition, plant NF-YBs and NF-YCs interact with other protein partners to recognize a plethora of genomic motifs, as the CCT protein family that binds CORE sites. The NF-Y subunit organization and its DNA-binding properties, together with the NF-Y HFD capacity to adapt different protein modules, represent plant-specific features that play a key role in development, growth and reproduction. Despite their relevance, these features are still poorly understood at the molecular level. Here, we present the structures of Arabidopsis and rice NF-YB/NF-YC dimers, and of an Arabidopsis NF-Y trimer in complex with the FT CCAAT box, together with biochemical data on NF-Y mutants. The dimeric structures identify the key residues for NF-Y HFD stabilization. The NF-Y/DNA structure and the mutation experiments shed light on HFD trimerization interface properties and the NF-YA sequence appetite for the bases flanking the CCAAT motif. These data explain the logic of plant NF-Y gene expansion: the trimerization adaptability and the flexible DNA-binding rules serve the scopes of accommodating the large number of NF-YAs, CCTs and possibly other NF-Y HFD binding partners and a diverse audience of genomic motifs.


  • Organizational Affiliation

    Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano, 20133, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OsGhd888Oryza sativaMutation(s): 0 
Gene Names: HD5DTH8GHD8HAP3HNFYB11Os08g0174500LOC_Os08g07740
UniProt
Find proteins for Q0J7P4 (Oryza sativa subsp. japonica)
Explore Q0J7P4 
Go to UniProtKB:  Q0J7P4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0J7P4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
OsNF-YC777Oryza sativaMutation(s): 0 
Gene Names: Os09g0480700OSNPB_090480700
UniProt
Find proteins for Q9XE33 (Oryza sativa subsp. japonica)
Explore Q9XE33 
Go to UniProtKB:  Q9XE33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XE33
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.836α = 90
b = 34.102β = 95.39
c = 67.081γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2021-03-03
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description