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PDBsum entry 4lbd

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Nuclear receptor PDB id
4lbd
Jmol
Contents
Protein chain
237 a.a. *
Ligands
961
Waters ×111
* Residue conservation analysis
PDB id:
4lbd
Name: Nuclear receptor
Title: Ligand-binding domain of the human retinoic acid receptor gamma bound to the synthetic agonist bms961
Structure: Retinoic acid receptor gamma. Chain: a. Fragment: lbd, ligand-binding domain, residues 178 - 423. Synonym: e domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Cell_line: bl21. Cellular_location: cytoplasm. Gene: hrargamma. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.50Å     R-factor:   0.183     R-free:   0.285
Authors: B.P.Klaholz,J.-P.Renaud,A.Mitschler,D.Moras,Structural Proteomics In Europe (Spine)
Key ref: B.P.Klaholz et al. (1998). Conformational adaptation of agonists to the human nuclear receptor RAR gamma. Nat Struct Biol, 5, 199-202. PubMed id: 9501913
Date:
04-Feb-98     Release date:   02-Mar-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P13631  (RARG_HUMAN) -  Retinoic acid receptor gamma
Seq:
Struc:
454 a.a.
237 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     steroid hormone mediated signaling pathway   3 terms 
  Biochemical function     DNA binding     4 terms  

 

 
Nat Struct Biol 5:199-202 (1998)
PubMed id: 9501913  
 
 
Conformational adaptation of agonists to the human nuclear receptor RAR gamma.
B.P.Klaholz, J.P.Renaud, A.Mitschler, C.Zusi, P.Chambon, H.Gronemeyer, D.Moras.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20097575 C.Bich, C.Bovet, N.Rochel, C.Peluso-Iltis, A.Panagiotidis, A.Nazabal, D.Moras, and R.Zenobi (2010).
Detection of nucleic acid-nuclear hormone receptor complexes with mass spectrometry.
  J Am Soc Mass Spectrom, 21, 635-645.  
  19471584 C.Rochette-Egly, and P.Germain (2009).
Dynamic and combinatorial control of gene expression by nuclear retinoic acid receptors (RARs).
  Nucl Recept Signal, 7, e005.  
18612831 D.C.Thompson, R.A.Denny, R.Nilakantan, C.Humblet, D.Joseph-McCarthy, and E.Feyfant (2008).
CONFIRM: connecting fragments found in receptor molecules.
  J Comput Aided Mol Des, 22, 761-772.  
17906643 A.R.de Lera, W.Bourguet, L.Altucci, and H.Gronemeyer (2007).
Design of selective nuclear receptor modulators: RAR and RXR as a case study.
  Nat Rev Drug Discov, 6, 811-820.  
17906642 L.Altucci, M.D.Leibowitz, K.M.Ogilvie, A.R.de Lera, and H.Gronemeyer (2007).
RAR and RXR modulation in cancer and metabolic disease.
  Nat Rev Drug Discov, 6, 793-810.  
17433757 S.Alvarez, P.Germain, R.Alvarez, F.Rodríguez-Barrios, H.Gronemeyer, and A.R.de Lera (2007).
Structure, function and modulation of retinoic acid receptor beta, a tumor suppressor.
  Int J Biochem Cell Biol, 39, 1406-1415.  
16170358 F.Piu, N.K.Gauthier, and F.Wang (2006).
Beta-arrestin 2 modulates the activity of nuclear receptor RAR beta2 through activation of ERK2 kinase.
  Oncogene, 25, 218-229.  
15709961 K.W.Nettles, and G.L.Greene (2005).
Ligand control of coregulator recruitment to nuclear receptors.
  Annu Rev Physiol, 67, 309-333.  
15528208 V.Pogenberg, J.F.Guichou, V.Vivat-Hannah, S.Kammerer, E.Pérez, P.Germain, A.R.de Lera, H.Gronemeyer, C.A.Royer, and W.Bourguet (2005).
Characterization of the interaction between retinoic acid receptor/retinoid X receptor (RAR/RXR) heterodimers and transcriptional coactivators through structural and fluorescence anisotropy studies.
  J Biol Chem, 280, 1625-1633.
PDB code: 1xdk
15576033 E.S.Manas, Z.B.Xu, R.J.Unwalla, and W.S.Somers (2004).
Understanding the selectivity of genistein for human estrogen receptor-beta using X-ray crystallography and computational methods.
  Structure, 12, 2197-2207.
PDB codes: 1x7j 1x7r
15520817 H.Gronemeyer, J.A.Gustafsson, and V.Laudet (2004).
Principles for modulation of the nuclear receptor superfamily.
  Nat Rev Drug Discov, 3, 950-964.  
15319780 P.Germain, S.Kammerer, E.Pérez, C.Peluso-Iltis, D.Tortolani, F.C.Zusi, J.Starrett, P.Lapointe, J.P.Daris, A.Marinier, A.R.de Lera, N.Rochel, and H.Gronemeyer (2004).
Rational design of RAR-selective ligands revealed by RARbeta crystal stucture.
  EMBO Rep, 5, 877-882.
PDB code: 1xap
15502323 S.Kammerer, P.Germain, R.Flaig, C.Peluso-Iltis, A.Mitschler, N.Rochel, H.Gronemeyer, and D.Moras (2004).
RARbeta ligand-binding domain bound to an SRC-1 co-activator peptide: purification, crystallization and preliminary X-ray diffraction analysis.
  Acta Crystallogr D Biol Crystallogr, 60, 2048-2050.  
12970175 S.Svensson, T.Ostberg, M.Jacobsson, C.Norström, K.Stefansson, D.Hallén, I.C.Johansson, K.Zachrisson, D.Ogg, and L.Jendeberg (2003).
Crystal structure of the heterodimeric complex of LXRalpha and RXRbeta ligand-binding domains in a fully agonistic conformation.
  EMBO J, 22, 4625-4633.
PDB code: 1uhl
12424754 S.Yamada, M.Shimizu, and K.Yamamoto (2003).
Structure-function relationships of vitamin D including ligand recognition by the vitamin D receptor.
  Med Res Rev, 23, 89.  
11963993 A.Ohno, M.Shimizu, and S.Yamada (2002).
Fluorinated vitamin D analogs to probe the conformation of vitamin D in its receptor complex: 19F-NMR studies and biological activity.
  Chem Pharm Bull (Tokyo), 50, 475-483.  
12220491 B.Klaholz, and D.Moras (2002).
C-H...O hydrogen bonds in the nuclear receptor RARgamma--a potential tool for drug selectivity.
  Structure, 10, 1197-1204.
PDB code: 1fd0
12009019 L.L.Issa, G.M.Leong, R.L.Sutherland, and J.A.Eisman (2002).
Vitamin D analogue-specific recruitment of vitamin D receptor coactivators.
  J Bone Miner Res, 17, 879-890.  
12142447 S.H.McLaughlin, and S.E.Jackson (2002).
Folding and stability of the ligand-binding domain of the glucocorticoid receptor.
  Protein Sci, 11, 1926-1936.  
12473098 Y.Xu, F.Fang, Y.Chu, D.Jones, and G.Jones (2002).
Activation of transcription through the ligand-binding pocket of the orphan nuclear receptor ultraspiracle.
  Eur J Biochem, 269, 6026-6036.  
11340063 A.C.Steinmetz, J.P.Renaud, and D.Moras (2001).
Binding of ligands and activation of transcription by nuclear receptors.
  Annu Rev Biophys Biomol Struct, 30, 329-359.  
11719067 G.Jones, M.Wozniak, Y.Chu, S.Dhar, and D.Jones (2001).
Juvenile hormone III-dependent conformational changes of the nuclear receptor ultraspiracle.
  Insect Biochem Mol Biol, 32, 33-49.  
11344298 G.Tocchini-Valentini, N.Rochel, J.M.Wurtz, A.Mitschler, and D.Moras (2001).
Crystal structures of the vitamin D receptor complexed to superagonist 20-epi ligands.
  Proc Natl Acad Sci U S A, 98, 5491-5496.
PDB codes: 1ie8 1ie9
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.  
10841540 B.P.Klaholz, A.Mitschler, M.Belema, C.Zusi, and D.Moras (2000).
Enantiomer discrimination illustrated by high-resolution crystal structures of the human nuclear receptor hRARgamma.
  Proc Natl Acad Sci U S A, 97, 6322-6327.
PDB codes: 1exa 1exx
10845098 J.Zhang, and M.A.Lazar (2000).
The mechanism of action of thyroid hormones.
  Annu Rev Physiol, 62, 439-466.  
10677485 K.Yamamoto, H.Masuno, M.Choi, K.Nakashima, T.Taga, H.Ooizumi, K.Umesono, W.Sicinska, J.VanHooke, H.F.DeLuca, and S.Yamada (2000).
Three-dimensional modeling of and ligand docking to vitamin D receptor ligand binding domain.
  Proc Natl Acad Sci U S A, 97, 1467-1472.  
10655475 M.Schapira, B.M.Raaka, H.H.Samuels, and R.Abagyan (2000).
Rational discovery of novel nuclear hormone receptor antagonists.
  Proc Natl Acad Sci U S A, 97, 1008-1013.  
10678179 N.Rochel, J.M.Wurtz, A.Mitschler, B.Klaholz, and D.Moras (2000).
The crystal structure of the nuclear receptor for vitamin D bound to its natural ligand.
  Mol Cell, 5, 173-179.
PDB code: 1db1
10835357 P.F.Egea, A.Mitschler, N.Rochel, M.Ruff, P.Chambon, and D.Moras (2000).
Crystal structure of the human RXRalpha ligand-binding domain bound to its natural ligand: 9-cis retinoic acid.
  EMBO J, 19, 2592-2601.
PDB code: 1fby
10882139 R.T.Gampe, V.G.Montana, M.H.Lambert, A.B.Miller, R.K.Bledsoe, M.V.Milburn, S.A.Kliewer, T.M.Willson, and H.E.Xu (2000).
Asymmetry in the PPARgamma/RXRalpha crystal structure reveals the molecular basis of heterodimerization among nuclear receptors.
  Mol Cell, 5, 545-555.
PDB codes: 1fm6 1fm9
10694383 S.Mailfait, D.Belaiche, M.Kouach, N.Dallery, P.Chavatte, P.Formstecher, and B.Sablonnière (2000).
Critical role of tyrosine 277 in the ligand-binding and transactivating properties of retinoic acid receptor alpha.
  Biochemistry, 39, 2183-2192.  
11050318 W.Bourguet, P.Germain, and H.Gronemeyer (2000).
Nuclear receptor ligand-binding domains: three-dimensional structures, molecular interactions and pharmacological implications.
  Trends Pharmacol Sci, 21, 381-388.  
10469641 A.C.Pike, A.M.Brzozowski, R.E.Hubbard, T.Bonn, A.G.Thorsell, O.Engström, J.Ljunggren, J.A.Gustafsson, and M.Carlquist (1999).
Structure of the ligand-binding domain of oestrogen receptor beta in the presence of a partial agonist and a full antagonist.
  EMBO J, 18, 4608-4618.
PDB codes: 1qkm 1qkn
  10082574 A.Mouchon, M.H.Delmotte, P.Formstecher, and P.Lefebvre (1999).
Allosteric regulation of the discriminative responsiveness of retinoic acid receptor to natural and synthetic ligands by retinoid X receptor and DNA.
  Mol Cell Biol, 19, 3073-3085.  
10600690 A.Mueller-Fahrnow, and U.Egner (1999).
Ligand-binding domain of estrogen receptors.
  Curr Opin Biotechnol, 10, 550-556.  
9876133 D.Kosztin, S.Izrailev, and K.Schulten (1999).
Unbinding of retinoic acid from its receptor studied by steered molecular dynamics.
  Biophys J, 76, 188-197.  
10421757 M.Géhin, V.Vivat, J.M.Wurtz, R.Losson, P.Chambon, D.Moras, and H.Gronemeyer (1999).
Structural basis for engineering of retinoic acid receptor isotype-selective agonists and antagonists.
  Chem Biol, 6, 519-529.  
  10548048 R.Pattanayek, and M.E.Newcomer (1999).
Protein and ligand adaptation in a retinoic acid binding protein.
  Protein Sci, 8, 2027-2032.  
10872460 R.V.Weatherman, R.J.Fletterick, and T.S.Scanlan (1999).
Nuclear-receptor ligands and ligand-binding domains.
  Annu Rev Biochem, 68, 559-581.  
9640540 D.Moras, and H.Gronemeyer (1998).
The nuclear receptor ligand-binding domain: structure and function.
  Curr Opin Cell Biol, 10, 384-391.  
9628869 J.Fagart, J.M.Wurtz, A.Souque, C.Hellal-Levy, D.Moras, and M.E.Rafestin-Oblin (1998).
Antagonism in the human mineralocorticoid receptor.
  EMBO J, 17, 3317-3325.  
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.