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 SOX9
Homo sapiens
 HIF1A
Homo sapiens
 Pax6
Mus musculus
 PAX6
Homo sapiens
 Snai2
Mus musculus
 PPARA
Homo sapiens
 Ppara
Mus musculus
 Thrb
Mus musculus
 SNAI2
Homo sapiens
 Tbr1
Mus musculus
Transcription Factor Encyclopedia  BETA
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Overview

The DNA binding domain of nuclear receptors is highly conserved throughout the superfamily (more than 40% amino acid identity over a 67-residue region) and is composed of two zinc fingers that fold to form a single structural unit. Each zinc finger contains a group of four Cys residues that co-ordinates a single zinc atom. An alpha helix at the end of the first zinc finger is inserted into the major groove of DNA and several residues engage in specific interactions with base pairs of the PuGGTCA motifs.[1] RAR-RXR heterodimers bind DNA with the RXR monomer bound 5' to the RAR monomer in DR2 and DR5 repeats, but in the reverse polarity on DR1 repeats, switching the activity of the heterodimer from activator to repressor of transcription.The dimeric interface on a DR5 element involves a region (D box) in the second zinc finger of the DNA binding domain of RXR and the tip of the RAR first zinc finger, while on a DR1 element association is mediated via the second zinc finger of RAR and the T box within the C-terminal extension of the RXR DNA binding domain.[2][3][4][5][6]

References
  1. Khorasanizadeh S and Rastinejad F. Nuclear-receptor interactions on DNA-response elements. Trends Biochem. Sci., 26(6):384-90. (PMID 11406412)
  2. Mader S et al. The patterns of binding of RAR, RXR and TR homo- and heterodimers to direct repeats are dictated by the binding specificites of the DNA binding domains. EMBO J., 12(13):5029-41. (PMID 8262045)
  3. Predki PF et al. Ordered binding of retinoic acid and retinoid-X receptors to asymmetric response elements involves determinants adjacent to the DNA-binding domain. Mol. Endocrinol., 8(1):31-9. (PMID 8152429)
  1. Zechel C et al. 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(6):1425-33. (PMID 8137826)
  2. Zechel C et al. 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(6):1414-24. (PMID 8137825)
  3. Rastinejad F et al. Structure of the RXR-RAR DNA-binding complex on the retinoic acid response element DR1. EMBO J., 19(5):1045-54. (PMID 10698945)
Structures
About this section
This section contains 3D PDB models of structural predictions for this transcription factor. METHODS: The template selection protocol follows that of Morozov and Siggia, in which templates are selected to optimize similarity of DNA-binding residues (Morozov AV, Siggia ED. PNAS 104(17):7068-73). This has been shown to increase modeling accuracy at the DNA-binding interface. For all solved structures containing DNA, amino acids within 4A of DNA (DNA-binding residues) are stored. Pfam domain hits of each DNA-bound chain are detected by hmmer, and each hit is added to a list mapping domain family name to chain hits. Pfam domain hits of each unsolved structure are detected by HMMER. For each identified Pfam family, the unsolved sequence is aligned to all solved family members (putative templates). Alignments are scored based on similarity of the DNA-binding residues in the template to the aligned residues of the unsolved sequence. For each subsequence of the unsolved protein identified as a DNA-binding domain, the top scoring template is selected. For sequences known to form homodimers, a homodimeric template is selected. The model is constructed from the template using Modeller 9v2. DNA bound to the template is added to the model by superimposition of the solved and modeled structures.
RARG 5916 2hanB
Image 3D Model .PDB File
Family
Zinc-coordinating Group » Hormone-nuclear Receptor Family
AR
Homo sapiens
Ar
Mus musculus
 ESR1
Homo sapiens
 Esr1
Mus musculus
 ESR2
Homo sapiens
 Esr2
Mus musculus
Esrra
Mus musculus
ESRRA
Homo sapiens
Esrrb
Mus musculus
ESRRB
Homo sapiens
Esrrg
Mus musculus
ESRRG
Homo sapiens
 HNF4A
Homo sapiens
 Hnf4a
Mus musculus
Hnf4g
Mus musculus
 HNF4G
Homo sapiens
Nr0b2
Mus musculus
NR0B2
Homo sapiens
Nr1d1
Mus musculus
NR1D1
Homo sapiens
Nr1d2
Mus musculus
NR1D2
Homo sapiens
Nr1h2
Mus musculus
NR1H2
Homo sapiens
Nr1h3
Mus musculus
NR1H3
Homo sapiens
Nr1h4
Mus musculus
NR1H4
Homo sapiens
Nr1h5
Mus musculus
Nr1i2
Mus musculus
NR1I2
Homo sapiens
 Nr1i3
Mus musculus
 NR1I3
Homo sapiens
Nr2c1
Mus musculus
NR2C1
Homo sapiens
Nr2c2
Mus musculus
NR2C2
Homo sapiens
 NR2E1
Homo sapiens
 Nr2e1
Mus musculus
Nr2e3
Mus musculus
NR2E3
Homo sapiens
 Nr2f1
Mus musculus
 NR2F1
Homo sapiens
 Nr2f2
Mus musculus
 NR2F2
Homo sapiens
Nr2f6
Mus musculus
NR2F6
Homo sapiens
 Nr3c1
Mus musculus
 NR3C1
Homo sapiens
Nr3c2
Mus musculus
NR3C2
Homo sapiens
Nr4a1
Mus musculus
NR4A1
Homo sapiens
Nr4a2
Mus musculus
NR4A2
Homo sapiens
Nr4a3
Mus musculus
NR4A3
Homo sapiens
Nr5a1
Mus musculus
NR5A1
Homo sapiens
Nr5a2
Mus musculus
NR5A2
Homo sapiens
Nr6a1
Mus musculus
NR6A1
Homo sapiens
Pgr
Mus musculus
PGR
Homo sapiens
 Ppara
Mus musculus
 PPARA
Homo sapiens
Ppard
Mus musculus
PPARD
Homo sapiens
 Pparg
Mus musculus
 PPARG
Homo sapiens
 Rara
Mus musculus
 RARA
Homo sapiens
 Rarb
Mus musculus
 RARB
Homo sapiens
 Rarg
Mus musculus
 RARG
Homo sapiens
Rora
Mus musculus
RORA
Homo sapiens
Rorb
Mus musculus
RORB
Homo sapiens
Rorc
Mus musculus
RORC
Homo sapiens
Rxra
Mus musculus
RXRA
Homo sapiens
Rxrb
Mus musculus
RXRB
Homo sapiens
Rxrg
Mus musculus
RXRG
Homo sapiens
Thra
Mus musculus
THRA
Homo sapiens
 Thrb
Mus musculus
 THRB
Homo sapiens
Vdr
Mus musculus
VDR
Homo sapiens
 
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