1CIT


Conserved Protein Domain Family
NR_DBD_NGFI-B

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cd06969: NR_DBD_NGFI-B 
Click on image for an interactive view with Cn3D
DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B
DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B) 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. NGFI-B interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. NGFI-B is a member of the nuclear-steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. NGFI-B binds to the NGFI-B response element (NBRE) 5'-(A/T)AAAGGTCA as a monomer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Statistics
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PSSM-Id: 143527
View PSSM: cd06969
Aligned: 13 rows
Threshold Bit Score: 125.25
Threshold Setting Gi: 4930008
Created: 2-Feb-2009
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:1CIT_A; C4 type zinc finger of Rattus norvegicus monomeric orphan nuclear receptor NGFI-B,contacts at 4A
    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:
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
Feature 1           #  #             #  #               #      #         #  #                 
1CIT_A          1 GRCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLA-NKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRT 75
gi 118343914  713 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKKSTYVCLA-NRNCPVDKRRRNRCQFCRFEKCLAVGMVKEVVRT 787
gi 115623739  386 GMCAVCGDSAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLA-NKNCTVDKRRRNRCQYCRFQKCLACGMVKEVVRT 460
gi 68132000   253 GTCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLA-SKNCPVDKRRRNRCQYCRFQKCLSVGMVKEVVRT 327
gi 118343916  484 GSCAVCGDKARWQHYGVLACEGCKGFFKRSVQKDARYVCLG-NSNCPIDKKTRTHCPYCRYQKCLRVGMIKNVVRT 558
gi 215504293  258 QLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKGAKYVCLA-NRDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRT 332
gi 548354     244 GRCAVCGDNASCQHYGVRTCEGCKGFFKRTVQKNAKYICLA-NKDCPVDKRRRNRCQFCRFQKCLVVGMVKEVVRT 318
gi 12644294   742 QLCAVCGDTAACQHYGVRTCEGCKGFFKRTVQKGSKYVCLA-DKNCPVDKRRRNRCQFCRFQKCLVVGMVKEVVRT 816
gi 194277579  246 QLCLVCGDNAACQHYGVRTCEGCKGFFKRTIQKNAQYVCLQ-AKNCVVDKRRRNRCQYCRFQKCLKVGMVKEVVRR 320
gi 156357575   13 EICAICLDKATGQHYGVTSCEGCKGFFKRSVQNKKDYTCRNlTKDCPIDKRHRNRCQYCRFQKCIQAGMIKEDAIP 88
gi 3929579    104 QPCSVCSDKAYVKHYGVFACEGCKGFFKRSVRNNRKYSCLG-KRHCDTDKKSRNRCQYCRFQKCVQVGMKPEAVQD 178
gi 17552670   266 KMCAVCNDRAVCLHYGARTCEGCKGFFKRTVQKNSKYTCAG-NKTCPIDKRYRSRCQYCRYQKCLEVGMVKEIVRH 340
gi 225196211  193 GTCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLA-NKNCPVDKRRRNRCQYCRFQKCLSVGMVKEVVRT 267

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