6QMP

NF-YB/C Heterodimer in Complex with NF-YA Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Constrained Peptides with Fine-Tuned Flexibility Inhibit NF-Y Transcription Factor Assembly.

Jeganathan, S.Wendt, M.Kiehstaller, S.Brancaccio, D.Kuepper, A.Pospiech, N.Carotenuto, A.Novellino, E.Hennig, S.Grossmann, T.N.

(2019) Angew Chem Int Ed Engl 58: 17351-17358

  • DOI: 10.1002/anie.201907901
  • Primary Citation of Related Structures:  
    6QMQ, 6QMP, 6QMS

  • PubMed Abstract: 
  • Protein complex formation depends on the interplay between preorganization and flexibility of the binding epitopes involved. The design of epitope mimetics typically focuses on stabilizing a particular bioactive conformation, often without considerin ...

    Protein complex formation depends on the interplay between preorganization and flexibility of the binding epitopes involved. The design of epitope mimetics typically focuses on stabilizing a particular bioactive conformation, often without considering conformational dynamics, which limits the potential of peptidomimetics against challenging targets such as transcription factors. We developed a peptide-derived inhibitor of the NF-Y transcription factor by first constraining the conformation of an epitope through hydrocarbon stapling and then fine-tuning its flexibility. In the initial set of constrained peptides, a single non-interacting α-methyl group was observed to have a detrimental effect on complex stability. Biophysical characterization revealed how this methyl group affects the conformation of the peptide in its bound state. Adaption of the methylation pattern resulted in a peptide that inhibits transcription factor assembly and subsequent recruitment to the target DNA.


    Organizational Affiliation

    Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081, HZ, Amsterdam, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear transcription factor Y subunit betaB95Homo sapiensMutation(s): 0 
Gene Names: NFYBHAP3
Find proteins for P25208 (Homo sapiens)
Explore P25208 
Go to UniProtKB:  P25208
NIH Common Fund Data Resources
PHAROS  P25208
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear transcription factor Y subunit gammaC96Homo sapiensMutation(s): 0 
Gene Names: NFYC
Find proteins for Q13952 (Homo sapiens)
Explore Q13952 
Go to UniProtKB:  Q13952
NIH Common Fund Data Resources
PHAROS  Q13952
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear transcription factor Y subunit alphaA31Homo sapiensMutation(s): 2 
Gene Names: NFYA
Find proteins for P23511 (Homo sapiens)
Explore P23511 
Go to UniProtKB:  P23511
NIH Common Fund Data Resources
PHAROS  P23511
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.9α = 90
b = 52.9β = 90
c = 134.1γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilBelgium678623

Revision History 

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Database references