5DX3

Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Stapled Peptide SRC2-P3 and Estradiol

• PDB DOI:  https://doi.org/10.2210/pdb5DX3/pdb

• Classification: Hormone receptor/peptide
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-09-23 Released: 2016-07-20 
• Deposition Author(s): Speltz, T.E., Fanning, S.W., Mayne, C.G., Tajkhorshid, E., Greene, G.L., Moore, T.W.
• Funding Organization(s): American Association of Colleges of Pharmacy, University of Illinois Cancer Center, Chicago Biomedical Consortium, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.257 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Literature

Stapled Peptides with gamma-Methylated Hydrocarbon Chains for the Estrogen Receptor/Coactivator Interaction.

Speltz, T.E., Fanning, S.W., Mayne, C.G., Fowler, C., Tajkhorshid, E., Greene, G.L., Moore, T.W.

(2016) Angew Chem Int Ed Engl 55: 4252-4255

• PubMed: 26928945 
• DOI: https://doi.org/10.1002/anie.201510557
• Primary Citation of Related Structures:  
  5DX3, 5DXB, 5DXE, 5DXG, 5HYR


• PubMed Abstract: 
  

"Stapled" peptides are typically designed to replace two non-interacting residues with a constraining, olefinic staple. To mimic interacting leucine and isoleucine residues, we have created new amino acids that incorporate a methyl group in the γ-position of the stapling amino acid S5. We have incorporated them into a sequence derived from steroid receptor coactivator 2, which interacts with estrogen receptor α. The best peptide (IC50 =89 nm) replaces isoleucine 689 with an S-γ-methyl stapled amino acid, and has significantly higher affinity than unsubstituted peptides (390 and 760 nm). Through X-ray crystallography and molecular dynamics studies, we show that the conformation taken up by the S-γ-methyl peptide minimizes the syn-pentane interactions between the α- and γ-methyl groups.

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Organizational Affiliation: 

Department of Medicinal Chemistry and Pharmacognosy and UI Cancer Center, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL, 60612, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 63.02 kDa 
• Atom Count: 3,969 
• Modelled Residue Count: 481 
• Deposited Residue Count: 548 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A	261	Homo sapiens	Mutation(s): 1  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	B	261	Homo sapiens	Mutation(s): 1  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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stapled Peptide SRC2-P3	C, D	13	Homo sapiens	Mutation(s): 0  Gene Names: NCOA2, BHLHE75, SRC2, TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EST	E [auth A], G [auth B]	ESTRADIOL C18 H24 O2 VOXZDWNPVJITMN-ZBRFXRBCSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
5GM	C, D	L-PEPTIDE LINKING	C8 H17 N O2		ILE
MK8	C, D	L-PEPTIDE LINKING	C7 H15 N O2		LEU

Binding Affinity Annotations
ID	Source	Binding Affinity
EST	BindingDB:  5DX3	Ki: min: 0.11, max: 100 (nM) from 13 assay(s)
		Kd: min: 0.2, max: 100 (nM) from 4 assay(s)
		IC50: min: 1.00e-2, max: 46 (nM) from 46 assay(s)
		EC50: min: 4.00e-3, max: 10 (nM) from 52 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.257 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.162	α = 90
b = 85.851	β = 109.09
c = 58.764	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Speltz, T.E., Fanning, S.W., Mayne, C.G., Tajkhorshid, E., Greene, G.L., Moore, T.W.

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Funding Organization	Location	Grant Number
American Association of Colleges of Pharmacy	United States	--
University of Illinois Cancer Center	United States	--
Chicago Biomedical Consortium	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41-GM104601
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)	United States	T32 AT007533
National Science Foundation (NSF, United States)	United States	MCA06N060

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Advisory, Author supporting evidence, Database references, Derived calculations
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2020-02-19
  Changes: Derived calculations