Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 62.55 kDa 
• Atom Count: 4056 
• Modelled Residue Count: 490 
• Deposited Residue Count: 542 
• Unique protein chains: 2

5KRF

Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the Dynamic WAY derivative, 1a

• PDB DOI: 10.2210/pdb5KRF/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-07-07 Released: 2017-02-15 
• Deposition Author(s): Nwachukwu, J.C., Srinivasan, S., Bruno, N.E., Nowak, J., Kojetin, D.J., Elemento, O., Katzenellenbogen, J.A., Nettles, K.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.266 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 

Literature

Systems Structural Biology Analysis of Ligand Effects on ER alpha Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies.

Nwachukwu, J.C., Srinivasan, S., Bruno, N.E., Nowak, J., Wright, N.J., Minutolo, F., Rangarajan, E.S., Izard, T., Yao, X.Q., Grant, B.J., Kojetin, D.J., Elemento, O., Katzenellenbogen, J.A., Nettles, K.W.

(2017) Cell Chem Biol 24: 35-45

• PubMed: 28042045 
• DOI: 10.1016/j.chembiol.2016.11.014
• Primary Citation of Related Structures:  
  5KR9, 5KRA, 5KRC, 5KRF, 5KRH, 5KRI, 5KRJ, 5KRK, 5KRL, 5KRM, 5KRO, 5TLD, 5TLF, 5TLG, 5TLL, 5TLM, 5TLO, 5TLP, 5TLT, 5TLU, 5TLV, 5TLX, 5TLY, 5TM1, 5TM2, 5TM3, 5TM4, 5TM5, 5TM6, 5TM7, 5TM8, 5TM9, 5TML, 5TMM, 5TMO, 5TMQ, 5TMR, 5TMS, 5TMT, 5TMU, 5TMV, 5TMW, 5TMZ, 5TN1, 5TN3, 5TN4, 5TN5, 5TN6, 5TN7, 5TN8


• PubMed Abstract: 
  

Environmental estrogens and anti-hormone therapies for breast cancer have diverse tissue- and signaling-pathway-selective outcomes, but how estrogen receptor alpha (ERα) mediates this phenotypic diversity is poorly understood. We implemented a statistical approach to allow unbiased, parallel analyses of multiple crystal structures, and identified subtle perturbations of ERα structure by different synthetic and environmental estrogens. Many of these perturbations were in the sub-Å range, within the noise of the individual structures, but contributed significantly to the activities of synthetic and environmental estrogens. Combining structural perturbation data from many structures with quantitative cellular activity profiles of the ligands enabled identification of structural rules for ligand-specific allosteric signaling-predicting activity from structure. This approach provides a framework for understanding the diverse effects of environmental estrogens and for guiding iterative medicinal chemistry efforts to generate improved breast cancer therapies, an approach that can be applied to understanding other ligand-regulated allosteric signaling pathways.

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Organizational Affiliation: 

Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	257	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 GTEx:  ENSG00000091831

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
KHKILHRLLQDSSS Peptide	C, D	14	synthetic construct	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
6WL	E [auth A], F [auth B]	4-[1-methyl-7-(trifluoromethyl)indazol-3-yl]benzene-1,3-diol C15 H11 F3 N2 O2 GRCDZFUAPCSCFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.266 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.361	α = 90
b = 80.875	β = 109.53
c = 58.113	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-07-07 
• Released Date: 2017-02-15 
Deposition Author(s): Nwachukwu, J.C., Srinivasan, S., Bruno, N.E., Nowak, J., Kojetin, D.J., Elemento, O., Katzenellenbogen, J.A., Nettles, K.W.

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release