6QMQ

NF-YB/C Heterodimer in Complex with NF-YA-derived Peptide Stabilized with C8-Hydrocarbon Linker

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.193 

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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear transcription factor Y subunit betaB95Homo sapiensMutation(s): 0 
Gene Names: NFYB, HAP3
Find proteins for P25208 (Homo sapiens)
Explore P25208 
Go to UniProtKB:  P25208
NIH Common Fund Data Resources
PHAROS  P25208
GTEx  ENSG00000120837
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
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
GTEx  ENSG00000066136
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear transcription factor Y subunit alphaA21Homo 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
GTEx  ENSG00000001167
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download Ideal Coordinates CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA		AL-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.01α = 90
b = 52.21β = 90
c = 72.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASESphasing

Structure Validation

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View more in-depth experimental data

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