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structure nameSTRUCTURE OF A YEAST TFIIA/TBP/TATA-BOX DNA COMPLEX
(TATA-BOX BINDING PROTEIN)
referenceGewirth et al. 'TO ? ? ?
sourceSACCHAROMYCES CEREVISIAE
experimentX-ray (resolution=2.50, R-factor=0.189)
structural superfamilyTATA-box binding protein-like;
sequence familyTranscription factor TFIID or TATAbinding;
multimeric complexes1rm1_AC 5fyw_ABMORU 5fz5_AMORUW 5oqj_7AMOQRU 5oqj_BX 5oqj_EW 5oqm_7AMOQRU 5oqm_EW 5sva_AZcdfjn 5sva_Bg 6eu0_ABEPVYZ 6f40_ABEOPUVW 6f41_ABEPUVW 6f42_ABO 6f42_UVW 6f44_BMOUVW 6gyk_MOU 6gyl_MOQRUW 6gym_7MOQRW 6gym_BU 7ml0_7AMOQRWX 7ml2_7MORU 7ml4_ABRW 7ml4_MOU 7o4i_7ABMOQRUWX 7o4j_7MOQRUWX 7o72_7AMOQRUWX 7o73_7ABMOQRUWX 7o75_7ABEMOQRUX 7zs9_257AMOQRUWXabcdefgh 7zsa_7ABMOQRUWXabcdefgh 7zsb_7ABMOQRUWXabcdefgh
redundant complexes7o4i 5oqj 5fyw 7ml0 7ml1 7ml2 6gyk 6f40 6f41 6f42 6f44 5sva 5oqm 7ml4 7o4j 7o72 7o73 7o75 7oh9 7oha 7ohb 5fz5 6gym 6gyl 6eu0 7q5b
reference complex5oqj_O
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureNVFLFVTNVFPLFVT

Estimated binding specificities ?

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# IC=8.431 IC/col=1.054 n_of_columns=8 specificity:   
A |  16   0  13   0   0  96   0  96
C |  13   0  16   0   0   0   0   0
G |  54   0  13   0   0   0   0   0
T |  13  96  54  96  96   0  96   0
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: TBP
TATAAAAGPubMed1rm1_A(2.57e-10), 1rm1_AC(2.64e-10), 5fyw_ABMORU(1.69e-04), ... (total=11)
TATAAAPubMed1rm1_A(3.65e-09), 1rm1_AC(3.74e-09), 5fyw_ABMORU(6.36e-06), ... (total=13)
TGTAAAPubMed1rm1_A(1.66e-04), 1rm1_AC(1.68e-04), 6eu0_ABEPVYZ(5.03e-03), ... (total=4)
CATAAAPubMed1rm1_A(1.75e-05), 1rm1_AC(1.78e-05), 5fyw_ABMORU(3.37e-03), ... (total=10)
TATTTAAAPubMed1rm1_A(3.11e-03), 1rm1_AC(3.14e-03), 5fyw_ABMORU(1.07e-03), ... (total=11)
GGGTATAAAAGGPubMed1rm1_A(4.59e-08), 1rm1_AC(4.68e-08), 5fyw_ABMORU(1.58e-03), ... (total=10)
TATATAPubMed1rm1_A(1.66e-04), 1rm1_AC(1.68e-04), 5fyw_ABMORU(6.36e-06), ... (total=9)
CTTTTPubMed1rm1_A(1.77e-03), 1rm1_AC(1.79e-03)
TATATAAPubMed1rm1_A(1.96e-06), 1rm1_AC(1.99e-06), 5fyw_ABMORU(2.50e-08), ... (total=12)
TATAAPubMed1rm1_A(1.62e-06), 1rm1_AC(1.62e-06), 5fyw_ABMORU(7.17e-07), ... (total=13)
AATAAAAGPubMed1rm1_A(1.16e-06), 1rm1_AC(1.18e-06), 5fyw_ABMORU(1.07e-03), ... (total=11)
TAAAAAPubMed1rm1_A(1.75e-05), 1rm1_AC(1.78e-05), 6eu0_ABEPVYZ(7.85e-07), ... (total=4)
term: TFIIA
TATAAAPubMed1rm1_A(3.65e-09), 1rm1_AC(3.74e-09), 5fyw_ABMORU(6.36e-06), ... (total=13)
CATAAAPubMed1rm1_A(1.75e-05), 1rm1_AC(1.78e-05), 5fyw_ABMORU(3.37e-03), ... (total=10)
TAAAAAPubMed1rm1_A(1.75e-05), 1rm1_AC(1.78e-05), 6eu0_ABEPVYZ(7.85e-07), ... (total=4)
TATATAPubMed1rm1_A(1.66e-04), 1rm1_AC(1.68e-04), 5fyw_ABMORU(6.36e-06), ... (total=9)
TATAAGPubMed1rm1_A(1.75e-05), 1rm1_AC(1.75e-05), 5fyw_ABMORU(6.36e-06), ... (total=13)
AATAAAAGPubMed1rm1_A(1.16e-06), 1rm1_AC(1.18e-06), 5fyw_ABMORU(1.07e-03), ... (total=11)
TATAAAAGPubMed1rm1_A(2.57e-10), 1rm1_AC(2.64e-10), 5fyw_ABMORU(1.69e-04), ... (total=11)
TTTAAAPubMed1rm1_A(1.66e-04), 1rm1_AC(1.68e-04), 6eu0_ABEPVYZ(5.85e-03), ... (total=4)
sitesourcematches (E-value)

Dendrogram of similar interfaces ?

matrix format
  
  NAVTFT--LTFAVATANTVTFAPALAFTVATA   L           +1ytb_A    
                                         +-------1 
  NTVAFC--LTFAVATTNAVTFTPALTFTVATA   L   !       +4wzs_D    
                                       --3 
  NTVTFA--LAFTVATTNAVTFTPALTFAVTTA   L   !       +4roc_B    
                                         +-------2 
  NAVAFTPALTFAVATA--VAFTPALTFAVAST   L           +1ais_A

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updated Mon Dec 18 05:57:37 2023