3e00 Summary

pdbe.org/3e00
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Intact PPAR gamma - RXR alpha Nuclear Receptor Complex on DNA bound with GW9662, 9-cis Retinoic Acid and NCOA2 Peptide

The structure was published by Chandra, V., Huang, P., Hamuro, Y., et al., Wang, Y., Burris, T.P., and Rastinejad, F., in 2008 in a paper entitled "Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 3.1 Å and deposited in 2008.

The experimental data on which the structure is based was also deposited.

This entry contains 12 copies of 5 unique biopolymers (complete list).

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule most likely forms heterohexamers.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A Retinoic acid receptor RXR-alpha P19793 (11-462) (RXRA_HUMAN)search Homo sapienssearch 98% 467 61%
D Peroxisome proliferator-activated receptor gamma P37231 (102-505) (PPARG_HUMAN)search Homo sapienssearch < 90% 419 86%
G NCOA2 Peptide Q15596 (685-697) (NCOA2_HUMAN)search Homo sapienssearch < 90% 13 76%
E NCOA2 Peptide Q15596 (685-697) (NCOA2_HUMAN)search Homo sapienssearch < 90% 13 76%


This entry contains 3 unique UniProt proteins:

UniProt accession Name Organism PDB
P19793 (11 - 462) Retinoic acid receptor RXR-alpha Homo sapiens
P37231 (102 - 505) Peroxisome proliferator-activated receptor gamma Homo sapiens
Q15596 (685 - 697) NCOA2 Peptide

Chain Structural classification (CATH) Sequence family (Pfam)
A (P19793) Erythroid Transcription Factor GATA-1, subunit Asearch, Retinoid X Receptorsearch PF00104: Ligand-binding domain of nuclear hormone receptorsearch, PF00105: Zinc finger, C4 type (two domains)search, PF11825: Nuclear/hormone receptor activator site AF-1search
D Erythroid Transcription Factor GATA-1, subunit Asearch, Retinoid X Receptorsearch Ligand-binding domain of nuclear hormone receptorsearch, Zinc finger, C4 type (two domains)search, PPAR gamma N-terminal regionsearch
G, E Steroid receptor coactivatorsearch

Chain ID Molecular function (GO) Cellular component (GO) Biological process (GO)
A (P19793) zinc ion bindingsearch protein bindingsearch DNA bindingsearch sequence-specific DNA binding transcription factor activitysearch sequence-specific DNA bindingsearch steroid hormone receptor activitysearch vitamin D response element bindingsearch protein heterodimerization activitysearch vitamin D receptor bindingsearch 9-cis retinoic acid receptor activitysearch retinoic acid-responsive element bindingsearch retinoic acid receptor activitysearch transcription regulatory region DNA bindingsearch ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activitysearch transcription factor bindingsearch RNA polymerase II regulatory region sequence-specific DNA bindingsearch metal ion bindingsearch transcription coactivator activitysearch chromatin DNA bindingsearch enzyme bindingsearch nucleussearch nuclear chromatinsearch nucleoplasmsearch vitamin metabolic processsearch response to retinoic acidsearch modulation by virus of host morphology or physiologysearch regulation of transcription from RNA polymerase II promotersearch negative regulation of transcription from RNA polymerase II promotersearch regulation of transcription, DNA-templatedsearch steroid hormone mediated signaling pathwaysearch cellular lipid metabolic processsearch heart developmentsearch cholesterol metabolic processsearch transcription initiation from RNA polymerase II promotersearch positive regulation of transcription, DNA-templatedsearch placenta developmentsearch ventricular cardiac muscle tissue morphogenesissearch ventricular cardiac muscle cell differentiationsearch transcription, DNA-templatedsearch cardiac muscle cell proliferationsearch in utero embryonic developmentsearch viral processsearch peroxisome proliferator activated receptor signaling pathwaysearch retinoic acid receptor signaling pathwaysearch positive regulation of transcription from RNA polymerase II promotersearch secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus developmentsearch maternal placenta developmentsearch camera-type eye developmentsearch embryo implantationsearch gene expressionsearch small molecule metabolic processsearch regulation of branching involved in prostate gland morphogenesissearch protein homotetramerizationsearch
D (P37231) sequence-specific DNA binding transcription factor activitysearch steroid hormone receptor activitysearch DNA bindingsearch zinc ion bindingsearch sequence-specific DNA bindingsearch ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activitysearch nucleussearch steroid hormone mediated signaling pathwaysearch regulation of transcription, DNA-templatedsearch

Chain InterPro annotation
A Retinoid X receptor/HNF4search Nuclear hormone receptor, ligand-binding, coresearch Zinc finger, nuclear hormone receptor-typesearch Steroid hormone receptorsearch Nuclear hormone receptor, ligand-bindingsearch Zinc finger, NHR/GATA-typesearch Nuclear/hormone receptor activator site AF-1search
D Nuclear hormone receptor, ligand-binding, coresearch Zinc finger, nuclear hormone receptor-typesearch Steroid hormone receptorsearch Peroxisome proliferator-activated receptorsearch Peroxisome proliferator-activated receptor, gammasearch Nuclear hormone receptor, ligand-bindingsearch Zinc finger, NHR/GATA-typesearch
G, E Nuclear receptor coactivator Src-1search Steroid receptor coactivatorsearch