4AWL

The NF-Y transcription factor is structurally and functionally a sequence specific histone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Sequence-Specific Transcription Factor NF-Y Displays Histone-Like DNA Binding and H2B-Like Ubiquitination.

Nardini, M.Gnesutta, N.Donati, G.Gatta, R.Forni, C.Fossati, A.Vonrhein, C.Moras, D.Romier, C.Bolognesi, M.Mantovani, R.

(2013) Cell 152: 132

  • DOI: 10.1016/j.cell.2012.11.047
  • Primary Citation of Related Structures:  
    4AWL

  • PubMed Abstract: 
  • The sequence-specific transcription factor NF-Y binds the CCAAT box, one of the sequence elements most frequently found in eukaryotic promoters. NF-Y is composed of the NF-YA and NF-YB/NF-YC subunits, the latter two hosting histone-fold domains (HFDs ...

    The sequence-specific transcription factor NF-Y binds the CCAAT box, one of the sequence elements most frequently found in eukaryotic promoters. NF-Y is composed of the NF-YA and NF-YB/NF-YC subunits, the latter two hosting histone-fold domains (HFDs). The crystal structure of NF-Y bound to a 25 bp CCAAT oligonucleotide shows that the HFD dimer binds to the DNA sugar-phosphate backbone, mimicking the nucleosome H2A/H2B-DNA assembly. NF-YA both binds to NF-YB/NF-YC and inserts an α helix deeply into the DNA minor groove, providing sequence-specific contacts to the CCAAT box. Structural considerations and mutational data indicate that NF-YB ubiquitination at Lys138 precedes and is equivalent to H2B Lys120 monoubiquitination, important in transcriptional activation. Thus, NF-Y is a sequence-specific transcription factor with nucleosome-like properties of nonspecific DNA binding and helps establish permissive chromatin modifications at CCAAT promoters. Our findings suggest that other HFD-containing proteins may function in similar ways.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ALPHAA78Homo sapiensMutation(s): 0 
Gene Names: NFYA
Find proteins for P23511 (Homo sapiens)
Explore P23511 
Go to UniProtKB:  P23511
NIH Common Fund Data Resources
PHAROS  P23511
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETAB94Homo sapiensMutation(s): 0 
Gene Names: NFYBHAP3
Find proteins for P25208 (Homo sapiens)
Explore P25208 
Go to UniProtKB:  P25208
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PHAROS  P25208
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMAC94Homo sapiensMutation(s): 0 
Gene Names: NFYC
Find proteins for Q13952 (Homo sapiens)
Explore Q13952 
Go to UniProtKB:  Q13952
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PHAROS  Q13952
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsLengthOrganismImage
HSP70 PROMOTER FRAGMENTI25Homo sapiens
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Entity ID: 5
MoleculeChainsLengthOrganismImage
HSP70 PROMOTER FRAGMENTJ25Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.7α = 90
b = 62.56β = 90
c = 139.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Experimental preparation, Other