PDBsum entry 1qkt

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Nuclear receptor PDB id
Protein chain
248 a.a. *
Waters ×395
* Residue conservation analysis
PDB id:
Name: Nuclear receptor
Title: Mutant estrogen nuclear receptor ligand binding domain complexed with estradiol
Structure: Estradiol receptor. Chain: a. Fragment: ligand binding domain, residues 304-551. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Cellular_location: nucleus. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PDB file)
2.20Å     R-factor:   0.223     R-free:   0.273
Authors: M.Ruff,M.Gangloff,S.Eiler,S.Duclaud,J.M.Wurtz,D.Moras
Key ref:
M.Gangloff et al. (2001). Crystal structure of a mutant hERalpha ligand-binding domain reveals key structural features for the mechanism of partial agonism. J Biol Chem, 276, 15059-15065. PubMed id: 11278577 DOI: 10.1074/jbc.M009870200
05-Aug-99     Release date:   18-Aug-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P03372  (ESR1_HUMAN) -  Estrogen receptor
595 a.a.
248 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     steroid hormone mediated signaling pathway   2 terms 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1074/jbc.M009870200 J Biol Chem 276:15059-15065 (2001)
PubMed id: 11278577  
Crystal structure of a mutant hERalpha ligand-binding domain reveals key structural features for the mechanism of partial agonism.
M.Gangloff, M.Ruff, S.Eiler, S.Duclaud, J.M.Wurtz, D.Moras.
The crystal structure of a triple cysteine to serine mutant ERalpha ligand-binding domain (LBD), complexed with estradiol, shows that despite the presence of a tightly bound agonist ligand, the protein exhibits an antagonist-like conformation, similar to that observed in raloxifen and 4-hydroxytamoxifen-bound structures. This mutated receptor binds estradiol with wild type affinity and displays transcriptional activity upon estradiol stimulation, but with limited potency (about 50%). This partial activity is efficiently repressed in antagonist competition assays. The comparison with available LBD structures reveals key features governing the positioning of helix H12 and highlights the importance of cysteine residues in promoting an active conformation. Furthermore the present study reveals a hydrogen bond network connecting ligand binding to protein trans conformation. These observations support a dynamic view of H12 positioning, where the control of the equilibrium between two stable locations determines the partial agonist character of a given ligand.
  Selected figure(s)  
Figure 3.
Fig. 3. Superposition of binding pockets of the wild type (yellow) and mutant (gray) structures. The estradiol A ring superposes perfectly in both structures, whereas the D-ring is slightly shifted.
Figure 5.
Fig. 5. a, effect of C417S mutation on H3. Superposition of wild type (yellow) and Cys Ser triple mutant (gray) emphasizing the shortening of H3 by one turn and the significant conformational change of the loop 1-3 are shown. b, effect of C530S mutation on H11. Superposition of wild type (yellow) and Cys Ser triple mutant (gray), showing the shortening of H11 on the mutant protein is shown. c, superposition of wild type (yellow) and triple mutant (gray) ER LBD structures near the mutated residues. The ligand is anchored by His^524 that interacts with the carboxyl group of Glu^419, a residue from L5-6. This glutamate contacts both the N-terminal end of H3 (Glu^339) and the C-terminal end of H11 (Lys^531). The hydrogen bond network connecting the estradiol O17, His^524 and Glu^419, Glu^339, Lys^531 in the wild type structure is shown. The effect of the C417S and C530S mutations are to shorten by one turn the N-terminal end of H3 and the C-terminal end of H11, respectively. This leads to the disruption of the hydrogen bond network. To confirm the relevance of this network, Glu^339, Glu^419, and Lys^531 were mutated in alanines and compared with Cys Ser mutant receptor in transactivation assays.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 15059-15065) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21220114 E.Wright, S.A.Busby, S.Wisecarver, J.Vincent, P.R.Griffin, and E.J.Fernandez (2011).
Helix 11 dynamics is critical for constitutive androstane receptor activity.
  Structure, 19, 37-44.  
20148675 P.Huang, V.Chandra, and F.Rastinejad (2010).
Structural overview of the nuclear receptor superfamily: insights into physiology and therapeutics.
  Annu Rev Physiol, 72, 247-272.  
20195256 S.I.O'Donoghue, D.S.Goodsell, A.S.Frangakis, F.Jossinet, R.A.Laskowski, M.Nilges, H.R.Saibil, A.Schafferhans, R.C.Wade, E.Westhof, and A.J.Olson (2010).
Visualization of macromolecular structures.
  Nat Methods, 7, S42-S55.  
19333551 S.Ellmann, H.Sticht, F.Thiel, M.W.Beckmann, R.Strick, and P.L.Strissel (2009).
Estrogen and progesterone receptors: from molecular structures to clinical targets.
  Cell Mol Life Sci, 66, 2405-2426.  
18391212 S.M.Soisson, G.Parthasarathy, A.D.Adams, S.Sahoo, A.Sitlani, C.Sparrow, J.Cui, and J.W.Becker (2008).
Identification of a potent synthetic FXR agonist with an unexpected mode of binding and activation.
  Proc Natl Acad Sci U S A, 105, 5337-5342.
PDB code: 3bej
18347588 S.Mader (2008).
Fast-tracking steroid receptor crystallization.
  Nat Chem Biol, 4, 226-227.  
  18097104 V.Cura, M.Gangloff, S.Eiler, D.Moras, and M.Ruff (2008).
Cleaved thioredoxin fusion protein enables the crystallization of poorly soluble ERalpha in complex with synthetic ligands.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 54-57.  
17400923 C.Bovet, A.Wortmann, S.Eiler, F.Granger, M.Ruff, B.Gerrits, D.Moras, and R.Zenobi (2007).
Estrogen receptor-ligand complexes measured by chip-based nanoelectrospray mass spectrometry: an approach for the screening of endocrine disruptors.
  Protein Sci, 16, 938-946.  
17999665 F.A.Pasha, M.M.Neaz, S.J.Cho, and S.B.Kang (2007).
Quantitative structure activity relationship (QSAR) study of estrogen derivatives based on descriptors of energy and softness.
  Chem Biol Drug Des, 70, 520-529.  
17311814 J.Yan, Y.S.Kim, X.P.Yang, M.Albers, M.Koegl, and A.M.Jetten (2007).
Ubiquitin-interaction motifs of RAP80 are critical in its regulation of estrogen receptor alpha.
  Nucleic Acids Res, 35, 1673-1686.  
16914190 P.Ascenzi, A.Bocedi, and M.Marino (2006).
Structure-function relationship of estrogen receptor alpha and beta: impact on human health.
  Mol Aspects Med, 27, 299-402.  
16782818 Y.Wang, N.Y.Chirgadze, S.L.Briggs, S.Khan, E.V.Jensen, and T.P.Burris (2006).
A second binding site for hydroxytamoxifen within the coactivator-binding groove of estrogen receptor beta.
  Proc Natl Acad Sci U S A, 103, 9908-9911.
PDB code: 2fsz
  15743715 A.Pillon, A.M.Boussioux, A.Escande, S.Aït-Aïssa, E.Gomez, H.Fenet, M.Ruff, D.Moras, F.Vignon, M.J.Duchesne, C.Casellas, J.C.Nicolas, and P.Balaguer (2005).
Binding of estrogenic compounds to recombinant estrogen receptor-alpha: application to environmental analysis.
  Environ Health Perspect, 113, 278-284.  
15521089 K.Fukuzawa, K.Kitaura, M.Uebayasi, K.Nakata, T.Kaminuma, and T.Nakano (2005).
Ab initio quantum mechanical study of the binding energies of human estrogen receptor alpha with its ligands: an application of fragment molecular orbital method.
  J Comput Chem, 26, 1.  
15123269 N.Fokialakis, G.Lambrinidis, D.J.Mitsiou, N.Aligiannis, S.Mitakou, A.L.Skaltsounis, H.Pratsinis, E.Mikros, and M.N.Alexis (2004).
A new class of phytoestrogens; evaluation of the estrogenic activity of deoxybenzoins.
  Chem Biol, 11, 397-406.  
12536206 B.C.Kallenberger, J.D.Love, V.K.Chatterjee, and J.W.Schwabe (2003).
A dynamic mechanism of nuclear receptor activation and its perturbation in a human disease.
  Nat Struct Biol, 10, 136-140.  
12665583 B.Farboud, H.Hauksdottir, Y.Wu, and M.L.Privalsky (2003).
Isotype-restricted corepressor recruitment: a constitutively closed helix 12 conformation in retinoic acid receptors beta and gamma interferes with corepressor recruitment and prevents transcriptional repression.
  Mol Cell Biol, 23, 2844-2858.  
14636576 R.Hartmann, J.Justesen, S.N.Sarkar, G.C.Sen, and V.C.Yee (2003).
Crystal structure of the 2'-specific and double-stranded RNA-activated interferon-induced antiviral protein 2'-5'-oligoadenylate synthetase.
  Mol Cell, 12, 1173-1185.
PDB code: 1px5
12077320 R.L.Rich, L.R.Hoth, K.F.Geoghegan, T.A.Brown, P.K.LeMotte, S.P.Simons, P.Hensley, and D.G.Myszka (2002).
Kinetic analysis of estrogen receptor/ligand interactions.
  Proc Natl Acad Sci U S A, 99, 8562-8567.  
11689423 C.Stehlin, J.M.Wurtz, A.Steinmetz, E.Greiner, R.Schüle, D.Moras, and J.P.Renaud (2001).
X-ray structure of the orphan nuclear receptor RORbeta ligand-binding domain in the active conformation.
  EMBO J, 20, 5822-5831.
PDB code: 1k4w
11607933 U.Egner, N.Heinrich, M.Ruff, M.Gangloff, A.Mueller-Fahrnow, and J.M.Wurtz (2001).
Different ligands-different receptor conformations: modeling of the hER alpha LBD in complex with agonists and antagonists.
  Med Res Rev, 21, 523-539.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.