Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47.20 kDa 
• Atom Count: 2600 
• Modelled Residue Count: 326 
• Deposited Residue Count: 419 
• Unique protein chains: 2

2OCF

Human estrogen receptor alpha ligand-binding domain in complex with estradiol and the E2#23 FN3 monobody

• PDB DOI: 10.2210/pdb2OCF/pdb

• Classification: HORMONE/GROWTH FACTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-12-20 Released: 2007-11-06 
• Deposition Author(s): Rajan, S.S., Kuruvilla, S.M., Sharma, S.K., Kim, Y., Huang, J., Koide, A., Koide, S., Joachimiak, A., Greene, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.251 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 

Literature

Probing protein conformational changes in living cells by using designer binding proteins: application to the estrogen receptor.

Koide, A., Abbatiello, S., Rothgery, L., Koide, S.

(2002) Proc Natl Acad Sci U S A 99: 1253-1258

• PubMed: 11818562 
• DOI: 10.1073/pnas.032665299
• Primary Citation of Related Structures:  
  2OCF


• PubMed Abstract: 
  

A challenge in understanding the mechanism of protein function in biology is to establish the correlation between functional form in the intracellular environment and high-resolution structures obtained with in vitro techniques. Here we present a strategy to probe conformational changes of proteins inside cells. Our method involves: (i) engineering binding proteins to different conformations of a target protein, and (ii) using them to sense changes in the surface property of the target in cells. We probed ligand-induced conformational changes of the estrogen receptor alpha (ER alpha) ligand-binding domain (LBD). By using yeast two-hybrid techniques, we first performed combinatorial library screening of "monobodies" (small antibody mimics using the scaffold of a fibronectin type III domain) for clones that bind to ER alpha and then characterized their interactions with ER alpha in the nucleus, the native environment of ER alpha, in the presence of various ligands. A library using a highly flexible loop yielded monobodies that specifically recognize a particular ligand complex of ER alpha, and the pattern of monobody specificity was consistent with the structural differences found in known crystal structures of ER alpha-LBD. A more restrained loop library yielded clones that bind both agonist- and antagonist-bound ER alpha. Furthermore, we found that a deletion of the ER alpha F domain that is C-terminally adjacent to the LBD increased the crossreactivity of monobodies to the apo-ER alpha-LBD, suggesting a dynamic nature of the ER alpha-LBD conformation and a role of the F domain in restraining the LBD in an inactive conformation.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY 14642, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A	298	Homo sapiens	Mutation(s): 3  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
Fibronectin	B [auth D]	121	Homo sapiens	Mutation(s): 8  Gene Names: CIG, FN1, FN
UniProt & NIH Common Fund Data Resources
Find proteins for P02751 (Homo sapiens) Explore P02751  Go to UniProtKB:  P02751
PHAROS:  P02751

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EST	C [auth A]	ESTRADIOL C18 H24 O2 VOXZDWNPVJITMN-ZBRFXRBCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
EST	BindingDB:  2OCF	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: 2.95 Å
• R-Value Free: 0.251 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.219	α = 90
b = 119.219	β = 90
c = 132.999	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
XFIT	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-12-20 
• Released Date: 2007-11-06 
Deposition Author(s): Rajan, S.S., Kuruvilla, S.M., Sharma, S.K., Kim, Y., Huang, J., Koide, A., Koide, S., Joachimiak, A., Greene, G.L.

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-08-03
  Changes: Database references
• Version 1.3: 2017-10-11
  Changes: Data collection
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations