PDBsum entry 1hra

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protein metals links
DNA-binding receptor PDB id
Protein chain
80 a.a. *
_ZN ×2
* Residue conservation analysis
PDB id:
Name: DNA-binding receptor
Title: The solution structure of the human retinoic acid receptor- beta DNA-binding domain
Structure: Retinoic acid receptor. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
NMR struc: 15 models
Authors: R.M.A.Knegtel,M.Katahira,J.G.Schilthuis,A.M.J.J.Bonvin, R.Boelens,D.Eib,P.T.Van Der Saag,R.Kaptein
Key ref: R.M.Knegtel et al. (1993). The solution structure of the human retinoic acid receptor-beta DNA-binding domain. J Biomol NMR, 3, 1. PubMed id: 8383553
25-Jul-93     Release date:   31-Jan-94    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P10826  (RARB_HUMAN) -  Retinoic acid receptor beta
455 a.a.
80 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  


J Biomol NMR 3:1 (1993)
PubMed id: 8383553  
The solution structure of the human retinoic acid receptor-beta DNA-binding domain.
R.M.Knegtel, M.Katahira, J.G.Schilthuis, A.M.Bonvin, R.Boelens, D.Eib, P.T.van der Saag, R.Kaptein.
The three-dimensional structure of the DNA-binding domain of the human retinoic acid receptor-beta (hRAR-beta) has been determined by nuclear magnetic resonance spectroscopy in conjunction with distance geometry, restrained molecular dynamics and iterative relaxation matrix calculations. A total of 1244 distance restraints were obtained from NOE intensities, of which 448 were intra-residue and 796 inter-residue restraints. In addition 23 chi and 30 phi dihedral angle restraints were obtained from J-coupling data. The two 'zinc-finger' regions of the 80-amino acid residue protein are followed by two alpha-helices that cross each other perpendicularly. There is a short stretch of b-sheet near the N-terminus. The alpha-helical core of the protein is well determined with a backbone root-mean-square deviation (r.m.s.d.) with respect to the average of 0.18 A and 0.37 A when the side chains of residues 31, 32, 36, 61, 62, 65 and 69 are included. The r.m.s.d. for the backbone of residues 5-80 is 0.76 A. For the first finger (residues 8-28), the r.m.s.d. of the backbone is 0.79 A. For the second finger (residues 44-62) the r.m.s.d. is 0.64 A. The overall structure is similar to that of the corresponding domain of the glucocorticoid receptor, although the C-terminal part of the protein is different. The second alpha-helix is two residues shorter and is followed by a well-defined region of extended backbone structure.

Literature references that cite this PDB file's key reference

  PubMed id Reference
10698945 F.Rastinejad, T.Wagner, Q.Zhao, and S.Khorasanizadeh (2000).
Structure of the RXR-RAR DNA-binding complex on the retinoic acid response element DR1.
  EMBO J, 19, 1045-1054.
PDB code: 1dsz
10913286 P.J.van Tilborg, M.Czisch, F.A.Mulder, G.E.Folkers, A.M.Bonvin, M.Nair, R.Boelens, and R.Kaptein (2000).
Changes in dynamical behavior of the retinoid X receptor DNA-binding domain upon binding to a 14 base-pair DNA half site.
  Biochemistry, 39, 8747-8757.  
9218433 D.S.Sem, D.R.Casimiro, S.A.Kliewer, J.Provencal, R.M.Evans, and P.E.Wright (1997).
NMR spectroscopic studies of the DNA-binding domain of the monomer-binding nuclear orphan receptor, human estrogen related receptor-2. The carboxyl-terminal extension to the zinc-finger region is unstructured in the free form of the protein.
  J Biol Chem, 272, 18038-18043.  
8663386 C.Rachez, P.Sautière, P.Formstecher, and P.Lefebvre (1996).
Identification of amino acids critical for the DNA binding and dimerization properties of the human retinoic acid receptor alpha. Importance of lysine 360, lysine 365, and valine 361.
  J Biol Chem, 271, 17996-18006.  
7559612 J.A.Lupisella, J.E.Driscoll, W.J.Metzler, and P.R.Reczek (1995).
The ligand binding domain of the human retinoic acid receptor gamma is predominantly alpha-helical with a Trp residue in the ligand binding site.
  J Biol Chem, 270, 24884-24890.  
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.
PDB code: 4aa6
  7823947 L.D.McBroom, G.Flock, and V.Giguère (1995).
The nonconserved hinge region and distinct amino-terminal domains of the ROR alpha orphan nuclear receptor isoforms are required for proper DNA bending and ROR alpha-DNA interactions.
  Mol Cell Biol, 15, 796-808.  
7704533 G.J.Kleywegt, T.Bergfors, H.Senn, P.Le Motte, B.Gsell, K.Shudo, and T.A.Jones (1994).
Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid.
  Structure, 2, 1241-1258.
PDB codes: 1cbq 1cbr 1cbs
8183888 J.Zilliacus, J.Carlstedt-Duke, J.A.Gustafsson, and A.P.Wright (1994).
Evolution of distinct DNA-binding specificities within the nuclear receptor family of transcription factors.
  Proc Natl Acad Sci U S A, 91, 4175-4179.  
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.  
16100953 J.W.Schwabe, L.Chapman, J.T.Finch, D.Rhodes, and D.Neuhaus (1993).
DNA recognition by the oestrogen receptor: from solution to the crystal.
  Structure, 1, 187-204.
PDB code: 1hcp
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