1rm1_A : 3D-footprint complex

structure name	STRUCTURE OF A YEAST TFIIA/TBP/TATA-BOX DNA COMPLEX (TATA-BOX BINDING PROTEIN)
reference	Gewirth et al. 'TO ? ? ?
source	SACCHAROMYCES CEREVISIAE
experiment	X-ray (resolution=2.50, R-factor=0.189)
structural superfamily	TATA-box binding protein-like;
sequence family	Transcription factor TFIID or TATAbinding;
redundant complexes	7o4i 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
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 1rm1_A interface=9,11,39,54,56,62,64,99,101,130,131,145,147,153,155, sgivptlqNiVatvtlgcrldlktvalharnaeynpkrFaavimrirepkttaLiFasgkmVvTgakseddsklasrkyariiqkigfaakftdfkiqNiVgscdvkfpirleglafshgtfssyepelFPgliyrmvkpkivlLiFvsgkiVlTgakqreeiyqafeaiypvlsefrkm
interface signature	NVFLFVTNVFPLFVT

Estimated binding specificities ?

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# IC=8.472 IC/col=1.059 n_of_columns=8

specificity:

A |   0  96   0  96  96  54  96  13
C |   0   0   0   0   0  13   0  57
G |   0   0   0   0   0  13   0  13
T |  96   0  96   0   0  16   0  13

scan!

Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: TBP
TATAAAAG	PubMed	1rm1_A(2.57e-10), 1rm1_AC(2.64e-10), 5fyw_ABMORU(1.69e-04), ... (total=11)
TATAAA	PubMed	1rm1_A(3.65e-09), 1rm1_AC(3.74e-09), 5fyw_ABMORU(6.36e-06), ... (total=13)
TGTAAA	PubMed	1rm1_A(1.66e-04), 1rm1_AC(1.68e-04), 6eu0_ABEPVYZ(5.03e-03), ... (total=4)
CATAAA	PubMed	1rm1_A(1.75e-05), 1rm1_AC(1.78e-05), 5fyw_ABMORU(3.37e-03), ... (total=10)
TATTTAAA	PubMed	1rm1_A(3.11e-03), 1rm1_AC(3.14e-03), 5fyw_ABMORU(1.07e-03), ... (total=11)
GGGTATAAAAGG	PubMed	1rm1_A(4.59e-08), 1rm1_AC(4.68e-08), 5fyw_ABMORU(1.58e-03), ... (total=10)
TATATA	PubMed	1rm1_A(1.66e-04), 1rm1_AC(1.68e-04), 5fyw_ABMORU(6.36e-06), ... (total=9)
CTTTT	PubMed	1rm1_A(1.77e-03), 1rm1_AC(1.79e-03)
TATATAA	PubMed	1rm1_A(1.96e-06), 1rm1_AC(1.99e-06), 5fyw_ABMORU(2.50e-08), ... (total=12)
TATAA	PubMed	1rm1_A(1.62e-06), 1rm1_AC(1.62e-06), 5fyw_ABMORU(7.17e-07), ... (total=13)
AATAAAAG	PubMed	1rm1_A(1.16e-06), 1rm1_AC(1.18e-06), 5fyw_ABMORU(1.07e-03), ... (total=11)
TAAAAA	PubMed	1rm1_A(1.75e-05), 1rm1_AC(1.78e-05), 6eu0_ABEPVYZ(7.85e-07), ... (total=4)
term: TFIIA
TATAAA	PubMed	1rm1_A(3.65e-09), 1rm1_AC(3.74e-09), 5fyw_ABMORU(6.36e-06), ... (total=13)
CATAAA	PubMed	1rm1_A(1.75e-05), 1rm1_AC(1.78e-05), 5fyw_ABMORU(3.37e-03), ... (total=10)
TAAAAA	PubMed	1rm1_A(1.75e-05), 1rm1_AC(1.78e-05), 6eu0_ABEPVYZ(7.85e-07), ... (total=4)
TATATA	PubMed	1rm1_A(1.66e-04), 1rm1_AC(1.68e-04), 5fyw_ABMORU(6.36e-06), ... (total=9)
TATAAG	PubMed	1rm1_A(1.75e-05), 1rm1_AC(1.75e-05), 5fyw_ABMORU(6.36e-06), ... (total=13)
AATAAAAG	PubMed	1rm1_A(1.16e-06), 1rm1_AC(1.18e-06), 5fyw_ABMORU(1.07e-03), ... (total=11)
TATAAAAG	PubMed	1rm1_A(2.57e-10), 1rm1_AC(2.64e-10), 5fyw_ABMORU(1.69e-04), ... (total=11)
TTTAAA	PubMed	1rm1_A(1.66e-04), 1rm1_AC(1.68e-04), 6eu0_ABEPVYZ(5.85e-03), ... (total=4)
site	source	matches (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 16 18:45:06 2024