1N1J

Crystal structure of the NF-YB/NF-YC histone pair

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

The NF-YB/NF-YC structure gives insight into DNA binding and transcription regulation by CCAAT factor NF-Y

Romier, C., Cocchiarella, F., Mantovani, R., Moras, D.

(2003) J Biol Chem 278: 1336-1345

  • DOI: 10.1074/jbc.M209635200
  • Primary Citation of Related Structures:  
    1N1J

  • PubMed Abstract: 

    • The heterotrimeric transcription factor NF-Y recognizes with high specificity and affinity the CCAAT regulatory element that is widely represented in promoters and enhancer regions. The CCAAT box acts in concert with neighboring elements, and its bending by NF-Y is thought to be a major mechanism required for transcription activation ...

    The heterotrimeric transcription factor NF-Y recognizes with high specificity and affinity the CCAAT regulatory element that is widely represented in promoters and enhancer regions. The CCAAT box acts in concert with neighboring elements, and its bending by NF-Y is thought to be a major mechanism required for transcription activation. We have solved the structure of the NF-YC/NF-YB subcomplex of NF-Y, which shows that the core domains of both proteins interact through histone fold motifs. This histone-like pair is closely related to the H2A/H2B and NC2alpha/NC2beta families, with features that are both common to this class of proteins and unique to NF-Y. The structure together with the modeling of the nonspecific interaction of NF-YC/NF-YB with DNA and the full NF-Y/CCAAT box complex highlight important structural features that account for different and possibly similar biological functions of the transcriptional regulators NF-Y and NC2. In particular, it emphasizes the role of the newly described alphaC helix of NF-YC, which is both important for NF-Y trimerization and a target for regulatory proteins, such as MYC and p53.

    Organizational Affiliation: 

    Département de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/Université Louis Pasteur, 1 Rue Laurent Fries, B.P. 10142, 67404 Illkirch Cedex, France.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NF-YBA93Homo sapiensMutation(s): 0 
Gene Names: NFYB, HAP3
UniProt & NIH Common Fund Data Resources
Find proteins for P25208 (Homo sapiens)
Explore P25208 
Go to UniProtKB:  P25208
PHAROS:  P25208
GTEx:  ENSG00000120837 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25208
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NF-YCB97Homo sapiensMutation(s): 0 
Gene Names: NFYC
UniProt & NIH Common Fund Data Resources
Find proteins for Q13952 (Homo sapiens)
Explore Q13952 
Go to UniProtKB:  Q13952
PHAROS:  Q13952
GTEx:  ENSG00000066136 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13952
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.624α = 90
b = 60.345β = 90
c = 61.645γ = 90
Software Package:
Software NamePurpose
ProDCdata collection
SCALEPACKdata scaling
SHARPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-04-16
    Changes: Other
  • Version 1.4: 2017-10-11
    Changes: Advisory, Refinement description