5M35

The molecular tweezer CLR01 stabilizes a disordered protein-protein interface


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

The Molecular Tweezer CLR01 Stabilizes a Disordered Protein-Protein Interface.

Bier, D.Mittal, S.Bravo-Rodriguez, K.Sowislok, A.Guillory, X.Briels, J.Heid, C.Bartel, M.Wettig, B.Brunsveld, L.Sanchez-Garcia, E.Schrader, T.Ottmann, C.

(2017) J. Am. Chem. Soc. 139: 16256-16263

  • DOI: 10.1021/jacs.7b07939
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein regions that are involved in protein-protein interactions (PPIs) very often display a high degree of intrinsic disorder, which is reduced during the recognition process. A prime example is binding of the rigid 14-3-3 adapter proteins to their ...

    Protein regions that are involved in protein-protein interactions (PPIs) very often display a high degree of intrinsic disorder, which is reduced during the recognition process. A prime example is binding of the rigid 14-3-3 adapter proteins to their numerous partner proteins, whose recognition motifs undergo an extensive disorder-to-order transition. In this context, it is highly desirable to control this entropy-costly process using tailored stabilizing agents. This study reveals how the molecular tweezer CLR01 tunes the 14-3-3/Cdc25CpS216 protein-protein interaction. Protein crystallography, biophysical affinity determination and biomolecular simulations unanimously deliver a remarkable finding: a supramolecular "Janus" ligand can bind simultaneously to a flexible peptidic PPI recognition motif and to a well-structured adapter protein. This binding fills a gap in the protein-protein interface, "freezes" one of the conformational states of the intrinsically disordered Cdc25C protein partner and enhances the apparent affinity of the interaction. This is the first structural and functional proof of a supramolecular ligand targeting a PPI interface and stabilizing the binding of an intrinsically disordered recognition motif to a rigid partner protein.


    Organizational Affiliation

    Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.,Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology , Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.,Department of Chemistry, University of Duisburg-Essen , Universitätsstrasse 7, 45117 Essen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
14-3-3 protein zeta/delta
A, B
229Homo sapiensMutation(s): 0 
Gene Names: YWHAZ
Find proteins for P63104 (Homo sapiens)
Go to Gene View: YWHAZ
Go to UniProtKB:  P63104
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
M-phase inducer phosphatase 3
C
10Homo sapiensMutation(s): 0 
Gene Names: CDC25C
EC: 3.1.3.48
Find proteins for P30307 (Homo sapiens)
Go to Gene View: CDC25C
Go to UniProtKB:  P30307
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
M-phase inducer phosphatase 3
D
7Homo sapiensMutation(s): 0 
Gene Names: CDC25C
EC: 3.1.3.48
Find proteins for P30307 (Homo sapiens)
Go to Gene View: CDC25C
Go to UniProtKB:  P30307
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BEZ
Query on BEZ

Download SDF File 
Download CCD File 
A, B
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
SEP
Query on SEP
C, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.221α = 90.00
b = 104.075β = 90.00
c = 114.451γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-10-14 
  • Released Date: 2017-11-15 
  • Deposition Author(s): Bier, D., Ottmann, C.
  • This entry supersedes: 5JIT

Funding OrganizationLocationGrant Number
German Research FoundationGermanyCollaborative Research Centre 1093
Netherlands Organisation for Scientific ResearchNetherlands024.001.035
Netherlands Organisation for Scientific ResearchNetherlands016.150.366

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Database references
  • Version 2.0: 2018-12-12
    Type: Atomic model, Data collection, Derived calculations, Source and taxonomy