2OCF

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorA298Homo sapiensMutation(s): 3 
Gene Names: ESR1ESRNR3A1
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
NIH Common Fund Data Resources
PHAROS:  P03372
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FibronectinB [auth D]121Homo sapiensMutation(s): 8 
Gene Names: CIGFN1FN
Find proteins for P02751 (Homo sapiens)
Explore P02751 
Go to UniProtKB:  P02751
NIH Common Fund Data Resources
PHAROS:  P02751
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EST
Query on EST

Download Ideal Coordinates CCD File 
C [auth A]ESTRADIOL
C18 H24 O2
VOXZDWNPVJITMN-ZBRFXRBCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
AL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ESTIC50:  2   nM  BindingDB
ESTEC50:  2.299999952316284   nM  BindingDB
ESTEC50:  0.5899999737739563   nM  BindingDB
ESTEC50:  0.009999999776482582   nM  BindingDB
ESTIC50:  1.5   nM  BindingDB
ESTIC50:  21.040000915527344   nM  BindingDB
ESTEC50:  5.699999809265137   nM  BindingDB
ESTKi:  2   nM  BindingDB
ESTIC50:  4   nM  BindingDB
ESTKd:  100   nM  BindingDB
ESTIC50:  3   nM  BindingDB
ESTIC50:  0.5   nM  BindingDB
ESTKi:  12   nM  BindingDB
ESTKi:  0.1599999964237213   nM  BindingDB
ESTKd:  0.20000000298023224   nM  BindingDB
ESTEC50:  0.10999999940395355   nM  BindingDB
ESTEC50:  0.699999988079071   nM  BindingDB
ESTEC50:  0.28999999165534973   nM  BindingDB
ESTIC50:  1   nM  BindingDB
ESTEC50:  0.47999998927116394   nM  BindingDB
ESTKi:  0.6499999761581421   nM  BindingDB
ESTEC50:  2.4000000953674316   nM  BindingDB
ESTIC50:  0.75   nM  BindingDB
ESTKi:  0.10999999940395355   nM  BindingDB
ESTEC50:  0.5600000023841858   nM  BindingDB
ESTEC50:  0.1599999964237213   nM  BindingDB
ESTIC50:  0.10999999940395355   nM  BindingDB
ESTIC50:  4.699999809265137   nM  BindingDB
ESTEC50:  1.100000023841858   nM  BindingDB
ESTIC50:  3.5999999046325684   nM  BindingDB
ESTEC50:  3.200000047683716   nM  BindingDB
ESTEC50:  0.07999999821186066   nM  BindingDB
ESTIC50:  1.2999999523162842   nM  BindingDB
ESTIC50:  0.3499999940395355   nM  BindingDB
ESTEC50:  2.200000047683716   nM  BindingDB
ESTIC50:  1.600000023841858   nM  BindingDB
ESTIC50:  1.899999976158142   nM  BindingDB
ESTIC50:  1.350000023841858   nM  BindingDB
ESTKi:  0.30000001192092896   nM  BindingDB
ESTIC50:  0.8999999761581421   nM  BindingDB
ESTIC50:  3.200000047683716   nM  BindingDB
ESTEC50:  3.799999952316284   nM  BindingDB
ESTEC50:  0.019999999552965164   nM  BindingDB
ESTIC50:  4.400000095367432   nM  BindingDB
ESTIC50:  0.44999998807907104   nM  BindingDB
ESTIC50:  0.699999988079071   nM  BindingDB
ESTEC50:  0.10000000149011612   nM  BindingDB
ESTKi:  0.18000000715255737   nM  BindingDB
ESTKi:  0.8299999833106995   nM  BindingDB
ESTIC50:  5.900000095367432   nM  BindingDB
ESTIC50:  0.8199999928474426   nM  BindingDB
ESTIC50:  1.7999999523162842   nM  BindingDB
ESTEC50:  0.20000000298023224   nM  BindingDB
ESTIC50:  0.5699999928474426   nM  BindingDB
ESTEC50:  10   nM  BindingDB
ESTKi:  0.20999999344348907   nM  BindingDB
ESTKi:  0.11999999731779099   nM  BindingDB
ESTIC50:  0.4099999964237213   nM  BindingDB
ESTKi:  2.200000047683716   nM  BindingDB
ESTIC50:  0.009999999776482582   nM  BindingDB
ESTEC50:  0.25999999046325684   nM  BindingDB
ESTIC50:  1.399999976158142   nM  BindingDB
ESTEC50:  0.07000000029802322   nM  BindingDB
ESTEC50:  0.05000000074505806   nM  BindingDB
ESTIC50:  5.699999809265137   nM  BindingDB
ESTIC50:  1.899999976158142   nM  BindingDB
ESTEC50:  1.0499999523162842   nM  BindingDB
ESTIC50:  2.200000047683716   nM  BindingDB
ESTIC50:  1.2000000476837158   nM  BindingDB
ESTKd:  3   nM  BindingDB
ESTIC50:  24   nM  BindingDB
ESTIC50:  28   nM  BindingDB
ESTEC50:  0.11999999731779099   nM  BindingDB
ESTKi:  100   nM  BindingDB
ESTEC50:  5.699999809265137   nM  BindingDB
ESTEC50:  0.75   nM  BindingDB
ESTIC50:  2   nM  BindingDB
ESTKi:  0.14000000059604645   nM  BindingDB
ESTIC50:  46   nM  BindingDB
ESTEC50:  0.3100000023841858   nM  BindingDB
ESTIC50:  4.800000190734863   nM  BindingDB
ESTIC50:  10   nM  BindingDB
ESTEC50:  0.09000000357627869   nM  BindingDB
ESTIC50:  3.4000000953674316   nM  BindingDB
ESTEC50:  0.49000000953674316   nM  BindingDB
ESTEC50:  0.3700000047683716   nM  BindingDB
ESTEC50:  1   nM  BindingDB
ESTEC50:  0.029999999329447746   nM  BindingDB
ESTEC50:  0.18000000715255737   nM  BindingDB
ESTEC50:  3   nM  BindingDB
ESTIC50:  18   nM  BindingDB
ESTEC50:  0.15000000596046448   nM  BindingDB
ESTIC50:  1.7000000476837158   nM  BindingDB
ESTIC50:  11   nM  BindingDB
ESTEC50:  2.7699999809265137   nM  BindingDB
ESTEC50:  0   nM  BindingDB
ESTIC50:  12.5   nM  BindingDB
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 = 119.219α = 90
b = 119.219β = 90
c = 132.999γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
XFITdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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