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structure nameCRYSTAL STRUCTURE OF THE T(-30) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.
(TRANSCRIPTION INITIATION FACTOR TFIID-1)
referencePatikoglou et al. 'Genes 13 3217 1999
sourceARABIDOPSIS THALIANA
experimentX-ray (resolution=1.80, R-factor=0.193)
structural superfamilyTATA-box binding protein-like;
sequence familyTranscription factor TFIID or TATAbinding;
multimeric complexes1vol_AB
redundant complexes1qn3_A 1qn4_A 1qn5_B 1qn6_B 1qn7_B 1qn8_B 1qn9_B 1qnb_A 1qnc_A 1qne_B 1vol_B 1vtl_E 1vto_A 6njq_B 6ueq_B
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureNVFLFVTNVFPLFVT

Estimated binding specificities ?

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# IC=8.069 IC/col=1.009 n_of_columns=8 specificity:   
A |  12   0  10   0   0  85  96  85
C |  64   0  10   0   0   0   0   0
G |  10   0  12   0   0   0   0  11
T |  10  96  64  96  96  11   0   0
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: TBP
TATAAAAGPubMed1qna_B(6.16e-09), 1vol_AB(1.01e-14), 6njq_B(1.18e-06), ... (total=17)
TATAAAPubMed1qna_B(1.82e-04), 1vol_AB(3.65e-09), 6njq_B(3.74e-09), ... (total=17)
TGTAAAPubMed1qna_B(1.82e-04), 1vol_AB(1.66e-04), 6njq_B(1.68e-04), ... (total=14)
TATAAPubMed1qna_B(1.01e-02), 1vol_AB(1.62e-06), 6njq_B(1.62e-06), ... (total=17)
CTTTTPubMed1qna_B(1.62e-06), 1vol_AB(2.22e-06), 6ueq_B(1.82e-06), ... (total=13)
GGGTATAAAAGGPubMed1qna_B(6.31e-07), 1vol_AB(9.47e-12), 6njq_B(4.55e-05), ... (total=17)
AATAAAAGPubMed1qna_B(1.23e-06), 1vol_AB(3.68e-10), 6njq_B(6.20e-04), ... (total=17)
CATAAAPubMed1qna_B(6.60e-03), 1vol_AB(1.75e-05), 6njq_B(1.78e-05), ... (total=16)
TATATAAPubMed1qna_B(5.57e-03), 1vol_AB(1.96e-06), 6njq_B(1.66e-04), ... (total=17)
TAAAAAPubMed1qna_B(1.86e-05), 1vol_AB(1.75e-05), 6njq_B(1.68e-04), ... (total=14)
TATTTAAAPubMed1qna_B(1.29e-06), 1vol_AB(3.11e-03), 6njq_B(3.14e-03), ... (total=15)
TATATAPubMed1vol_AB(1.66e-04), 6njq_B(1.68e-04), 6ueq_B(2.36e-04), ... (total=13)
sitesourcematches (E-value)

Dendrogram of similar interfaces ?

matrix format
  
  NTVTFT--LTFAVATTNAVTFTPALTFAVATA   L                      +1qna_B    
                                              +-------------3 
  NTVTFT--LTFAVATTNAVTFAPALTFTVATA   L   +----4             +7nvu_O    
                                         !    ! 
  NTVAFT--LTFAVATTNAVAFAPALTFTVATA   L   !    +--------------1rm1_A    
                                         ! 
  NAVTFT--LTFAVATANTVTFAPALAFTVATA   L --6                       +1ytb_A    
                                         !                     +-1 
  NTVAFC--LTFAVATTNAVTFTPALTFTVATA   L   ! +-------------------2 +4wzs_D    
                                         ! !                   ! 
  NTVTFA--LAFTVATTNAVTFTPALTFAVTTA       +-5                   +4roc_B    
                                           ! 
  NAVAFTPALTFAVATA--VAFTPALTFAVAST   L     +-------------------1ais_A

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updated Fri Sep 13 15:56:45 2024