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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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
  • 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 ...

    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: 

    Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorD [auth C],
E [auth D],
A [auth F]		15Homo sapiensMutation(s): 0 
Gene Names: ESR1, ESR, NR3A1
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
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C8L
Query on C8L
Download Ideal Coordinates CCD File 
G [auth C]Cucurbit[8]uril
C48 H48 N32 O16
CONWISUOKHSUDR-LBCLZKRDSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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 


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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