5Y7W | pdb_00005y7w

Crystal structure of the Nco-A1 PAS-B domain with YL-2

• PDB DOI: https://doi.org/10.2210/pdb5Y7W/pdb

• Classification: TRANSCRIPTION/INIHIBITOR
• Organism(s): Mus musculus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-18 Released: 2017-11-15 
• Deposition Author(s): Lee, Y.J., Yoon, H.S., Lee, J.H., Bae, J.H., Song, J.Y., Lim, H.S.
• Funding Organization(s): National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.204 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Targeted Inhibition of the NCOA1/STAT6 Protein-Protein Interaction

Lee, Y., Yoon, H., Hwang, S.M., Shin, M.K., Lee, J.H., Oh, M., Im, S.H., Song, J., Lim, H.S.

(2017) J Am Chem Soc 139: 16056-16059

• PubMed: 29090910 
• DOI: https://doi.org/10.1021/jacs.7b08972
• Primary Citation Related Structures: 
  5Y7W


• PubMed Abstract: 
  

  The complex formation between transcription factors (TFs) and coactivator proteins is required for transcriptional activity, and thus disruption of aberrantly activated TF/coactivator interactions could be an attractive therapeutic strategy. However, modulation of such protein-protein interactions (PPIs) has proven challenging. Here we report a cell-permeable, proteolytically stable, stapled helical peptide directly targeting nuclear receptor coactivator 1 (NCOA1), a coactivator required for the transcriptional activity of signal transducer and activator of transcription 6 (STAT6). We demonstrate that this stapled peptide disrupts the NCOA1/STAT6 complex, thereby repressing STAT6-mediated transcription. Furthermore, we solved the first crystal structure of a stapled peptide in complex with NCOA1. The stapled peptide therefore represents an invaluable chemical probe for understanding the precise role of the NCOA1/STAT6 interaction and an excellent starting point for the development of a novel class of therapeutic agents.

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Organizational Affiliation: 
• Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea.
New Drug Development Center, Daegu Gyeongbuk Medical Innovation Foundation , Daegu 41061, South Korea.
Division of Integrative Biosciences & Biotechnology, POSTECH , Pohang 37673, South Korea.
Academy of Immunology and Microbiology, Institute for Basic Science (IBS) , Pohang 37673, South Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.67 kDa 
• Atom Count: 2,184 
• Modeled Residue Count: 265 
• Deposited Residue Count: 286 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	A, B	127	Mus musculus	Mutation(s): 0  Gene Names: Ncoa1, Src1 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for P70365 (Mus musculus) Explore P70365  Go to UniProtKB:  P70365
IMPC:  MGI:1276523

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
YL-2 peptide	C, D	16	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALC	C, D	L-PEPTIDE LINKING	C9 H17 N O2		ALA
MK8	C, D	L-PEPTIDE LINKING	C7 H15 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.204 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.501	α = 90
b = 62.501	β = 90
c = 137.177	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Lee, Y.J., Yoon, H.S., Lee, J.H., Bae, J.H., Song, J.Y., Lim, H.S.

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Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017R1A2B3004941
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017M3A9G4052952

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2017-11-29
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary