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: 2.5 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.188 

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:  

  • PubMed Abstract: 

    • Protein complex formation highly depends on the interplay between preorganization and flexibility of involved binding epitopes. The design of epitope mimetics mainly focuses on the stabilization of a particular bioactive conformation often not consid ...

    Protein complex formation highly depends on the interplay between preorganization and flexibility of involved binding epitopes. The design of epitope mimetics mainly focuses on the stabilization of a particular bioactive conformation often not considering the conformational dynamics. This limits the potential of peptidomimetics in particular when aiming for challenging targets such as transcription factors. Here, we report the first peptide-derived inhibitor of the NF-Y transcription factor by first constraining the conformation of an epitope using the hydrocarbon stapling approach and then fine-tuning its flexibility. In the initial set of constrained peptides, we observed a severe effect of a single non-interacting α-methyl group on complex stability. The combination of X-ray and NMR structures as well as isothermal titration calorimetry and CD spectroscopy reveal how this methyl group affects the conformation of the peptide in its bound state. Adaption of the methylation pattern results in a peptide which inhibits transcription factor assembly and its subsequent recruitment to the target DNA. These results highlight the importance of residual conformational freedom when constraining protein fragments in their bioactive conformation.

    Organizational Affiliation: 

    CGC Dortmund, GERMANY.,University of Naples "Federico II", ITALY.,VU University Amsterdam, NETHERLANDS.,University of Naples Federico II, ITALY.,VU Universtity Amsterdam, Chemistry and Pharmaceutical Sciences, De Boelelaan 1108, 1081 HZ, Amsterdam, NETHERLANDS.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear transcription factor Y subunit beta
B
95Homo sapiensMutation(s): 0 
Gene Names: NFYB (HAP3)
Find proteins for P25208 (Homo sapiens)
Go to Gene View: NFYB
Go to UniProtKB:  P25208
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear transcription factor Y subunit gamma
C
96Homo sapiensMutation(s): 0 
Gene Names: NFYC
Find proteins for Q13952 (Homo sapiens)
Go to Gene View: NFYC
Go to UniProtKB:  Q13952
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nuclear transcription factor Y subunit alpha
A
21Homo sapiensMutation(s): 0 
Gene Names: NFYA
Find proteins for P23511 (Homo sapiens)
Go to Gene View: NFYA
Go to UniProtKB:  P23511
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
A
L-PEPTIDE LINKINGC4 H9 N O2ALA
NH2
Query on NH2
A
NON-POLYMERH2 N

--

MKD
Query on MKD
A
L-PEPTIDE LINKINGC9 H19 N O2

--

ACE
Query on ACE
A
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.010α = 90.00
b = 52.210β = 90.00
c = 72.990γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASESphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


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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
    Type: Data collection, Database references
  • Version 1.2: 2019-11-27
    Type: Database references