5N10

Cucurbit[8]uril and 14-3-3 based binary bivalent supramolecular-protein assembly platform


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 2.2 of the entry. See complete history

Literature

A Binary Bivalent Supramolecular Assembly Platform Based on Cucurbit[8]uril and Dimeric Adapter Protein 14-3-3.

de Vink, P.J.Briels, J.M.Schrader, T.Milroy, L.G.Brunsveld, L.Ottmann, C.

(2017) Angew. Chem. Int. Ed. Engl. 56: 8998-9002

  • DOI: 10.1002/anie.201701807

  • PubMed Abstract: 
  • Interactions between proteins frequently involve recognition sequences based on multivalent binding events. Dimeric 14-3-3 adapter proteins are a prominent example and typically bind partner proteins in a phosphorylation-dependent mono- or bivalent m ...

    Interactions between proteins frequently involve recognition sequences based on multivalent binding events. Dimeric 14-3-3 adapter proteins are a prominent example and typically bind partner proteins in a phosphorylation-dependent mono- or bivalent manner. Herein we describe the development of a cucurbit[8]uril (Q8)-based supramolecular system, which in conjunction with the 14-3-3 protein dimer acts as a binary and bivalent protein assembly platform. We fused the phenylalanine-glycine-glycine (FGG) tripeptide motif to the N-terminus of the 14-3-3-binding epitope of the estrogen receptor α (ERα) for selective binding to Q8. Q8-induced dimerization of the ERα epitope augmented its affinity towards 14-3-3 through a binary bivalent binding mode. The crystal structure of the Q8-induced ternary complex revealed molecular insight into the multiple supramolecular interactions between the protein, the peptide, and Q8.


    Organizational Affiliation

    Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, 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
Estrogen receptor
F, C, D
15Homo sapiensMutation(s): 0 
Gene Names: ESR1 (ESR, NR3A1)
Find proteins for P03372 (Homo sapiens)
Go to Gene View: ESR1
Go to UniProtKB:  P03372
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
14-3-3 protein beta/alpha
A
246Homo sapiensMutation(s): 0 
Gene Names: YWHAB
Find proteins for P31946 (Homo sapiens)
Go to Gene View: YWHAB
Go to UniProtKB:  P31946
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
14-3-3 protein beta/alpha
B
249Homo sapiensMutation(s): 0 
Gene Names: YWHAB
Find proteins for P31946 (Homo sapiens)
Go to Gene View: YWHAB
Go to UniProtKB:  P31946
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
C8L
Query on C8L

Download SDF File 
Download CCD File 
C
Cucurbit[8]uril
C48 H48 N32 O16
CONWISUOKHSUDR-LBCLZKRDSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
C, D, F
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 133.807α = 90.00
b = 57.571β = 98.64
c = 93.450γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
iMOSFLMdata reduction
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organization for Scientific ResearchNetherlands024.001.035
Netherlands Organization for Scientific ResearchNetherlands016.150.366
German Research FoundationGermanyCRC1093

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 2.0: 2017-08-02
    Type: Atomic model, Database references
  • Version 2.1: 2017-09-06
    Type: Author supporting evidence
  • Version 2.2: 2019-10-16
    Type: Data collection