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Transcription regulation PDB id
1hcp
Jmol
Contents
Protein chain
75 a.a. *
Metals
_ZN ×2
* Residue conservation analysis
PDB id:
1hcp
Name: Transcription regulation
Title: DNA recognition by the oestrogen receptor: from solution to the crystal
Structure: Human/chicken estrogen receptor. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: chicken protein has identical amino acid sequence
NMR struc: 30 models
Authors: J.W.R.Schwabe,D.Rhodes,D.Neuhaus
Key ref:
J.W.Schwabe et al. (1993). DNA recognition by the oestrogen receptor: from solution to the crystal. Structure, 1, 187-204. PubMed id: 16100953 DOI: 10.1016/0969-2126(93)90020-H
Date:
23-Nov-93     Release date:   23-Nov-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03372  (ESR1_HUMAN) -  Estrogen receptor
Seq:
Struc: 		 
Seq:
Struc: 		595 a.a.
75 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     5 terms  

 

 
DOI no: 10.1016/0969-2126(93)90020-H Structure 1:187-204 (1993)
PubMed id: 16100953  
 
 
DNA recognition by the oestrogen receptor: from solution to the crystal.
J.W.Schwabe, L.Chapman, J.T.Finch, D.Rhodes, D.Neuhaus.
 
  ABSTRACT  
 
BACKGROUND: The steroid/nuclear hormone receptors are a large family of conserved ligand-activated transcription factors that regulate gene expression through binding to response elements upstream of their target genes. Most members of this family bind to DNA as homodimers or heterodimers and recognize the sequence, spacing and orientation of the two half-sites of their response elements. The recognition and discrimination of the sequence and arrangements of these half-sites are mediated primarily by a highly conserved DNA-binding domain. RESULTS: Here we describe the DNA-binding properties of the isolated DNA-binding domain of the oestrogen receptor, the ERDBD, and its refined NMR structure. This domain is monomeric in solution, but two molecules bind cooperatively to specific DNA sequences; this cooperativity determines the arrangement of half-sites that is recognized by the ERDBD. The 10 carboxy-terminal residues and a region of 15 residues within the domain are disordered in the solution structure, yet are important for DNA binding. CONCLUSION: The cooperative nature of ERDBD binding to DNA is important. The previously-determined X-ray structure of the ERDBD dimer bound to DNA shows that the 15 internal residues disordered in solution make contact both with DNA and with the corresponding region of the other monomer. These results suggest that these residues become ordered during the process of binding to DNA, forming the dimer interface and thus contributing to the cooperative interaction between monomers.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20047966 C.E.Mason, F.J.Shu, C.Wang, R.M.Session, R.G.Kallen, N.Sidell, T.Yu, M.H.Liu, E.Cheung, and C.B.Kallen (2010).
Location analysis for the estrogen receptor-alpha reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements.
  Nucleic Acids Res, 38, 2355-2368.  
17426379 R.P.Metpally, R.Vigneshwar, and R.Sowdhamini (2007).
Genome inventory and analysis of nuclear hormone receptors in Tetraodon nigroviridis.
  J Biosci, 32, 43-50.  
10522700 M.R.Tremblay, J.Simard, and D.Poirier (1999).
Parallel solid-phase synthesis of a model library of 7alpha-alkylamide estradiol derivatives as potential estrogen receptor antagonists.
  Bioorg Med Chem Lett, 9, 2827-2832.  
9478126 J.P.Mackay, and M.Crossley (1998).
Zinc fingers are sticking together.
  Trends Biochem Sci, 23, 1-4.  
  9528764 J.R.Wood, G.L.Greene, and A.M.Nardulli (1998).
Estrogen response elements function as allosteric modulators of estrogen receptor conformation.
  Mol Cell Biol, 18, 1927-1934.  
9251777 D.Kosztin, T.C.Bishop, and K.Schulten (1997).
Binding of the estrogen receptor to DNA. The role of waters.
  Biophys J, 73, 557-570.  
9241421 G.Patikoglou, and S.K.Burley (1997).
Eukaryotic transcription factor-DNA complexes.
  Annu Rev Biophys Biomol Struct, 26, 289-325.  
9302989 J.W.Schwabe, and D.Rhodes (1997).
Linkers made to measure.
  Nat Struct Biol, 4, 680-683.  
9083662 S.Izrailev, S.Stepaniants, M.Balsera, Y.Oono, and K.Schulten (1997).
Molecular dynamics study of unbinding of the avidin-biotin complex.
  Biophys J, 72, 1568-1581.  
  8807884 J.A.Katzenellenbogen, and B.S.Katzenellenbogen (1996).
Nuclear hormone receptors: ligand-activated regulators of transcription and diverse cell responses.
  Chem Biol, 3, 529-536.  
  7735836 J.W.Schwabe, L.Chapman, and D.Rhodes (1995).
The oestrogen receptor recognizes an imperfectly palindromic response element through an alternative side-chain conformation.
  Structure, 3, 201-213.  
7696496 M.A.Eriksson, T.Härd, and L.Nilsson (1995).
Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution.
  Biophys J, 68, 402-426.  
7664086 N.D.Arbuckle, and B.Luisi (1995).
A recipe for specificity.
  Nat Struct Biol, 2, 341-346.  
  8137826 C.Zechel, X.Q.Shen, J.Y.Chen, Z.P.Chen, P.Chambon, and H.Gronemeyer (1994).
The dimerization interfaces formed between the DNA binding domains of RXR, RAR and TR determine the binding specificity and polarity of the full-length receptors to direct repeats.
  EMBO J, 13, 1425-1433.  
  8137825 C.Zechel, X.Q.Shen, P.Chambon, and H.Gronemeyer (1994).
Dimerization interfaces formed between the DNA binding domains determine the cooperative binding of RXR/RAR and RXR/TR heterodimers to DR5 and DR4 elements.
  EMBO J, 13, 1414-1424.  
  7922039 D.N.Jones, M.A.Searles, G.L.Shaw, M.E.Churchill, S.S.Ner, J.Keeler, A.A.Travers, and D.Neuhaus (1994).
The solution structure and dynamics of the DNA-binding domain of HMG-D from Drosophila melanogaster.
  Structure, 2, 609-627.
PDB code: 1hma
7925381 M.S.Lee, D.S.Sem, S.A.Kliewer, J.Provencal, R.M.Evans, and P.E.Wright (1994).
NMR assignments and secondary structure of the retinoid X receptor alpha DNA-binding domain. Evidence for the novel C-terminal helix.
  Eur J Biochem, 224, 639-650.  
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.