2YJD

Stapled peptide bound to Estrogen Receptor Beta

• PDB DOI: https://doi.org/10.2210/pdb2YJD/pdb

• Classification: HORMONE RECEPTOR/PEPTIDE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-19 Released: 2011-08-03 
• Deposition Author(s): Phillips, C., Roberts, L.R., Schade, M., Bent, A., Davies, N.L., Moore, R., Pannifer, A.D., Brown, D.G., Pickford, A.R., Irving, S.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.260 
• R-Value Work: 0.225 
• R-Value Observed: 0.226 

Literature

Design and Structure of Stapled Peptides Binding to Estrogen Receptors.

Phillips, C., Roberts, L.R., Schade, M., Bazin, R., Bent, A., Davies, N.L., Moore, R., Pannifer, A.D., Pickford, A.R., Prior, S.H., Read, C.M., Scott, A., Brown, D.G., Xu, B., Irving, S.L.

(2011) J Am Chem Soc 133: 9696

• PubMed: 21612236 
• DOI: https://doi.org/10.1021/ja202946k
• Primary Citation of Related Structures:  
  2LDA, 2LDC, 2LDD, 2YJA, 2YJD


• PubMed Abstract: 
  

  Synthetic peptides that specifically bind nuclear hormone receptors offer an alternative approach to small molecules for the modulation of receptor signaling and subsequent gene expression. Here we describe the design of a series of novel stapled peptides that bind the coactivator peptide site of estrogen receptors. Using a number of biophysical techniques, including crystal structure analysis of receptor-stapled peptide complexes, we describe in detail the molecular interactions and demonstrate that all-hydrocarbon staples modulate molecular recognition events. The findings have implications for the design of stapled peptides in general.

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Organizational Affiliation: 

Department of Chemistry, Pfizer, Sandwich CT13 9NJ, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
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: 57.47 kDa 
• Atom Count: 3,960 
• Modelled Residue Count: 472 
• Deposited Residue Count: 506 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESTROGEN RECEPTOR BETA	A, B	240	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens) Explore Q92731  Go to UniProtKB:  Q92731
PHAROS:  Q92731 GTEx:  ENSG00000140009

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
STAPLED PEPTIDE	C, D	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596 GTEx:  ENSG00000140396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YJD	E [auth A], F [auth B]	4-(2-PROPAN-2-YLOXYBENZIMIDAZOL-1-YL)PHENOL C16 H16 N2 O2 IRWOSCQWORJIQP-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MK8	C, D	L-PEPTIDE LINKING	C7 H15 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.260 
• R-Value Work: 0.225 
• R-Value Observed: 0.226 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.62	α = 90
b = 102.62	β = 90
c = 102.62	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-03 
Deposition Author(s): Phillips, C., Roberts, L.R., Schade, M., Bent, A., Davies, N.L., Moore, R., Pannifer, A.D., Brown, D.G., Pickford, A.R., Irving, S.L.

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Atomic model, Other
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary