8QU3

NF-YB/C Heterodimer in Complex with a 13-mer NF-YA-derived Peptide Stabilized with C8-Hydrocarbon Linker


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Binding Dynamics of a Stapled Peptide Targeting the Transcription Factor NF-Y.

Durukan, C.Arbore, F.Klintrot, R.Bigiotti, C.Ilie, I.M.Vreede, J.Grossmann, T.N.Hennig, S.

(2024) Chembiochem 25: e202400020-e202400020

  • DOI: https://doi.org/10.1002/cbic.202400020
  • Primary Citation of Related Structures:  
    8QU2, 8QU3, 8QU4

  • PubMed Abstract: 

    Transcription factors (TFs) play a central role in gene regulation, and their malfunction can result in a plethora of severe diseases. TFs are therefore interesting therapeutic targets, but their involvement in protein-protein interaction networks and the frequent lack of well-defined binding pockets render them challenging targets for classical small molecules. As an alternative, peptide-based scaffolds have proven useful, in particular with an α-helical active conformation. Peptide-based strategies often require extensive structural optimization efforts, which could benefit from a more detailed understanding of the dynamics in inhibitor/protein interactions. In this study, we investigate how truncated stapled α-helical peptides interact with the transcription factor Nuclear Factor-Y (NF-Y). We identified a 13-mer minimal binding core region, for which two crystal structures with an altered C-terminal peptide conformation when bound to NF-Y were obtained. Subsequent molecular dynamics simulations confirmed that the C-terminal part of the stapled peptide is indeed relatively flexible while still showing defined interactions with NF-Y. Our findings highlight the importance of flexibility in the bound state of peptides, which can contribute to overall binding affinity.


  • Organizational Affiliation

    Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear transcription factor Y subunit alpha15Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for P23511 (Homo sapiens)
Explore P23511 
Go to UniProtKB:  P23511
PHAROS:  P23511
GTEx:  ENSG00000001167 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23511
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear transcription factor Y subunit beta95Homo sapiensMutation(s): 0 
Gene Names: NFYBHAP3
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
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear transcription factor Y subunit gamma96Homo 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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MK8
Query on MK8
A
L-PEPTIDE LINKINGC7 H15 N O2LEU
NLE
Query on NLE
A
L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.75α = 90
b = 51.39β = 90
c = 72.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing
XSCALEdata scaling
XDSdata reduction
GDAdata collection

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Structure summary