2A66,2NLL,2HAN,2EBL,2C7A,1LO1,3CBB,1R0O,1KB6,3DZU,1CIT,1DSZ,1HCQ,1R4I,1HLZ,1R4R,3DZU


Conserved Protein Domain Family
NR_DBD_like

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cd06916: NR_DBD_like 
Click on image for an interactive view with Cn3D
DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers.
Statistics
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PSSM-Id: 143512
View PSSM: cd06916
Aligned: 58 rows
Threshold Bit Score: 96.0916
Threshold Setting Gi: 114793589
Created: 8-Jan-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
zinc bindingDNA binding
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1:zinc binding site [ion binding site]
Evidence:
  • Structure:2A66_A; zinc binding site of Human Liver Receptor Dna Binding Domain defined by 4A contacts.
    View structure with Cn3D
  • Comment:Zinc finger, C4-type: The domain contains two groups of four Cys residues. Each group is involved in the co-ordination of a single zinc atom.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1        #  #             #  #                 #            #         #  #               
2A66_A        12 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNn--kRYTCIen-------qnCQIDKTQRKRCPYCRFQKCLSVGMKLEAV 82  human
2C7A_A         5 CLICGDEASGCHYGVLTCGSCKVFFKRAMEGq--hNYLCAgr-------ndCIVDKIRRKNCPACRLRKCCQAGMVLGGR 75  human
1LO1_A         7 CLVCGDIASGYHYGVASCEACKAFFKRTIQGn--iEYSCPat-------neCEITKRRRKSCQACRFMKALKVGMLKEGV 77  human
1HCQ_A         7 CAVCNDYASGYHYGVWSCEGCKAFFKRSIQGh--nDYMCPat-------nqCTIDKNRRKSCQACRLRKCYEVGMMKGGI 77  human
1R4I_A        10 CLICGDEASGAHYGALTCGSCKVFFKRAAEGk--qKYLCAsr-------ndCTIDKFRRKNCPSCRLRKCYEAGMTLGAR 80  Norway rat
ACB10649     184 CAVCHCPSTGLHYGVYACEGCKSFFHRAHKRa--hPYVCPan-------nnCVIDRRLKKNCPACRLKKCLAMGMSFEEH 254 Florida lancelet
XP_001636937   7 CAVCGDESSGYHYGAYTCEGCKSFFKRTVQRglvkKYSCVrsn-----qnqCPMDKNSRAKCQACRLQRCFDAGMVLNGV 81  starlet sea ane...
AAF68669     209 CMVCGDCAHGFHYGVVTCEGCKGFFRRTVQRn--lRYSCHks-------srCEINRQTRTRCQACRYQQCLMLACHYDVR 279 Trichinella spi...
Q10902       105 CMVCGDNSTGYHYGVQSCEGCKGFFRRSVHKn--iAYVCTkgenctfsyenCAANRGVRTRCQACRFAKCLAVGMNRDNV 182 nematode
1R4R_A         7 CLVCSDEASGCHYGVLTCGSCKVFFKRAVEGq--hNYLCAgr-------ndCIIDKIRRKNCPACRYRKCLQAGMNLEAR 77  Norway rat
Feature 1         
2A66_A        83 R 83  human
2C7A_A        76 K 76  human
1LO1_A        78 R 78  human
1HCQ_A        78 R 78  human
1R4I_A        81 K 81  Norway rat
ACB10649     255 A 255 Florida lancelet
XP_001636937  82 R 82  starlet sea anemone
AAF68669     280 I 280 Trichinella spiralis
Q10902       183 R 183 nematode
1R4R_A        78 K 78  Norway rat

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