Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 

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

Macromolecule Content

• Total Structure Weight: 62.52 kDa 
• Atom Count: 4894 
• Residue Count: 490 
• 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)
• Mutation(s): No 


• 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: 1.60 Å
• R-Value Free: 0.194 
• R-Value Work: 0.170 
• R-Value Observed: 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
• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	C, D, F	15	Homo sapiens	Mutation(s): 0  Gene Names: ESR1, ESR, NR3A1
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
NIH Common Fund Data Resources
PHAROS  P03372 GTEx  ENSG00000091831

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein beta/alpha	A	246	Homo sapiens	Mutation(s): 0  Gene Names: YWHAB
Find proteins for P31946 (Homo sapiens) Explore P31946  Go to UniProtKB:  P31946
NIH Common Fund Data Resources
PHAROS  P31946 GTEx  ENSG00000166913

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein beta/alpha	B	249	Homo sapiens	Mutation(s): 0  Gene Names: YWHAB
Find proteins for P31946 (Homo sapiens) Explore P31946  Go to UniProtKB:  P31946
NIH Common Fund Data Resources
PHAROS  P31946 GTEx  ENSG00000166913

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C8L	C	Cucurbit[8]uril C48 H48 N32 O16 CONWISUOKHSUDR-LBCLZKRDSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-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: 1.60 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 = 133.807	α = 90
b = 57.571	β = 98.64
c = 93.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
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
  Changes: Atomic model, Database references
• Version 2.1: 2017-09-06
  Changes: Author supporting evidence
• Version 2.2: 2019-10-16
  Changes: Data collection