PDBsum entry 3dzy

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protein dna_rna ligands metals Protein-protein interface(s) links
Transcription/DNA PDB id
Protein chains
302 a.a. *
354 a.a. *
_ZN ×4
* Residue conservation analysis
PDB id:
Name: Transcription/DNA
Title: Intact ppar gamma - rxr alpha nuclear receptor complex on dn with rosiglitazone, 9-cis retinoic acid and ncoa2 peptide
Structure: Retinoic acid receptor rxr-alpha. Chain: a. Fragment: unp residues 11-462. Synonym: retinoid x receptor alpha, nuclear receptor subfam group b member 1. Engineered: yes. Peroxisome proliferator-activated receptor gamma. Chain: d. Fragment: unp residues 102-505.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: rxra, nr2b1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: pparg, nr1c3. Synthetic: yes. Other_details: synthetic DNA.
3.10Å     R-factor:   0.213     R-free:   0.268
Authors: V.Chandra,P.Huang,Y.Hamuro,S.Raghuram,Y.Wang,T.P.Burris,F.Ra
Key ref: V.Chandra et al. (2008). Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA. Nature, 456, 350-356. PubMed id: 19043829
30-Jul-08     Release date:   28-Oct-08    
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Protein chain
Pfam   ArchSchema ?
P19793  (RXRA_HUMAN) -  Retinoic acid receptor RXR-alpha
462 a.a.
302 a.a.
Protein chain
Pfam   ArchSchema ?
P37231  (PPARG_HUMAN) -  Peroxisome proliferator-activated receptor gamma
505 a.a.
354 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     receptor complex   5 terms 
  Biological process     viral reproduction   30 terms 
  Biochemical function     RNA polymerase II regulatory region sequence-specific DNA binding     20 terms  


Nature 456:350-356 (2008)
PubMed id: 19043829  
Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA.
V.Chandra, P.Huang, Y.Hamuro, S.Raghuram, Y.Wang, T.P.Burris, F.Rastinejad.
Nuclear receptors are multi-domain transcription factors that bind to DNA elements from which they regulate gene expression. The peroxisome proliferator-activated receptors (PPARs) form heterodimers with the retinoid X receptor (RXR), and PPAR-gamma has been intensively studied as a drug target because of its link to insulin sensitization. Previous structural studies have focused on isolated DNA or ligand-binding segments, with no demonstration of how multiple domains cooperate to modulate receptor properties. Here we present structures of intact PPAR-gamma and RXR-alpha as a heterodimer bound to DNA, ligands and coactivator peptides. PPAR-gamma and RXR-alpha form a non-symmetric complex, allowing the ligand-binding domain (LBD) of PPAR-gamma to contact multiple domains in both proteins. Three interfaces link PPAR-gamma and RXR-alpha, including some that are DNA dependent. The PPAR-gamma LBD cooperates with both DNA-binding domains (DBDs) to enhance response-element binding. The A/B segments are highly dynamic, lacking folded substructures despite their gene-activation properties.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21478866 J.Zhang, M.J.Chalmers, K.R.Stayrook, L.L.Burris, Y.Wang, S.A.Busby, B.D.Pascal, R.D.Garcia-Ordonez, J.B.Bruning, M.A.Istrate, D.J.Kojetin, J.A.Dodge, T.P.Burris, and P.R.Griffin (2011).
DNA binding alters coactivator interaction surfaces of the intact VDR-RXR complex.
  Nat Struct Mol Biol, 18, 556-563.  
21478865 N.Rochel, F.Ciesielski, J.Godet, E.Moman, M.Roessle, C.Peluso-Iltis, M.Moulin, M.Haertlein, P.Callow, Y.Mély, D.I.Svergun, and D.Moras (2011).
Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings.
  Nat Struct Mol Biol, 18, 564-570.  
20657587 D.Kim, B.J.Blus, V.Chandra, P.Huang, F.Rastinejad, and S.Khorasanizadeh (2010).
Corecognition of DNA and a methylated histone tail by the MSL3 chromodomain.
  Nat Struct Mol Biol, 17, 1027-1029.
PDB codes: 3m9p 3m9q 3oa6
19487700 M.L.Privalsky, S.Lee, J.B.Hahm, B.M.Young, R.N.Fong, and I.H.Chan (2009).
The p160 coactivator PAS-B motif stabilizes nuclear receptor binding and contributes to isoform-specific regulation by thyroid hormone receptors.
  J Biol Chem, 284, 19554-19563.  
19622862 T.Oyama, K.Toyota, T.Waku, Y.Hirakawa, N.Nagasawa, J.I.Kasuga, Y.Hashimoto, H.Miyachi, and K.Morikawa (2009).
Adaptability and selectivity of human peroxisome proliferator-activated receptor (PPAR) pan agonists revealed from crystal structures.
  Acta Crystallogr D Biol Crystallogr, 65, 786-795.
PDB codes: 2znn 2zno 2znp 2znq
19888307 Y.Pan, C.J.Tsai, B.Ma, and R.Nussinov (2009).
How do transcription factors select specific binding sites in the genome?
  Nat Struct Mol Biol, 16, 1118-1120.  
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