Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62519.83 
• Atom Count: 4342 
• Residue Count: 540 
• Unique protein chains: 3

5N10

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

• DOI: 10.2210/pdb5N10/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2017-02-04 Released: 2017-05-24 
• Deposition Author(s): de Vink, P.J., Ottmann, C.
• Funding Organization(s): Netherlands Organization for Scientific Research; German Research Foundation 

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Experimental Data Snapshot

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

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

• PubMed: 28510303 
• 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 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.

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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  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Estrogen receptor	F, C, D	15	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
14-3-3 protein beta/alpha	A	246	Homo sapiens	Mutation(s): 0  Gene Names: YWHAB
Find proteins for P31946 (Homo sapiens) Go to Gene View: YWHAB Go to UniProtKB:  P31946

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
14-3-3 protein beta/alpha	B	249	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
C8L	C	Cucurbit[8]uril C48 H48 N32 O16 CONWISUOKHSUDR-LBCLZKRDSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	C, D, F	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

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 = 133.807	α = 90.00
b = 57.571	β = 98.64
c = 93.450	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-02-04 
• Released Date: 2017-05-24 
• Deposition Author(s): de Vink, P.J., Ottmann, C.

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Funding Organization	Location	Grant Number
Netherlands Organization for Scientific Research	Netherlands	024.001.035
Netherlands Organization for Scientific Research	Netherlands	016.150.366
German Research Foundation	Germany	CRC1093

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