5N10

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

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Ligand Structure Quality Assessment 


This is version 2.3 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: https://doi.org/10.1002/anie.201701807
  • Primary Citation of Related Structures:  
    5N10

  • 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 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.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen receptorA [auth F],
D [auth C],
E [auth D]
15Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
PHAROS:  P03372
GTEx:  ENSG00000091831 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
14-3-3 protein beta/alphaB [auth A]246Homo sapiensMutation(s): 0 
Gene Names: YWHAB
UniProt & NIH Common Fund Data Resources
Find proteins for P31946 (Homo sapiens)
Explore P31946 
Go to UniProtKB:  P31946
PHAROS:  P31946
GTEx:  ENSG00000166913 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31946
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
14-3-3 protein beta/alphaC [auth B]249Homo sapiensMutation(s): 0 
Gene Names: YWHAB
UniProt & NIH Common Fund Data Resources
Find proteins for P31946 (Homo sapiens)
Explore P31946 
Go to UniProtKB:  P31946
PHAROS:  P31946
GTEx:  ENSG00000166913 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31946
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A [auth F],
D [auth C],
E [auth D]
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.807α = 90
b = 57.571β = 98.64
c = 93.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 2.0: 2017-08-02
    Changes: Atomic model, Database references
  • Version 2.1: 2017-09-06
    Changes: Author supporting evidence
  • Version 2.2: 2019-10-16
    Changes: Data collection
  • Version 2.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description