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Conserved domains on  [gi|394953994|ref|NP_001257417|]
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transcription initiation factor TFIID subunit 11 isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HFD_SF super family cl45933
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 108-137 1.12e-14

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.


The actual alignment was detected with superfamily member pfam04719:

Pssm-ID: 480273  Cd Length: 86  Bit Score: 64.81  E-value: 1.12e-14
                          10        20        30
                  ....*....|....*....|....*....|
gi 394953994  108 ILVSSFSEEQLNRYEMYRRSAFPKAAIKRH 137
Cdd:pfam04719   1 LLLSNFSEEQLDRYEVFRRSSFNKAVIKKL 30
 
Name Accession Description Interval E-value
TAFII28 pfam04719
hTAFII28-like protein conserved region; The general transcription factor, TFIID, consists of ...
 108-137 1.12e-14

hTAFII28-like protein conserved region; The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C-terminal of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3.


Pssm-ID: 428086  Cd Length: 86  Bit Score: 64.81  E-value: 1.12e-14
                          10        20        30
                  ....*....|....*....|....*....|
gi 394953994  108 ILVSSFSEEQLNRYEMYRRSAFPKAAIKRH 137
Cdd:pfam04719   1 LLLSNFSEEQLDRYEVFRRSSFNKAVIKKL 30
HFD_TAF11 cd08048
histone-fold domain found in transcription initiation factor TFIID subunit 11 (TAF11) and ...
 113-136 2.07e-11

histone-fold domain found in transcription initiation factor TFIID subunit 11 (TAF11) and similar proteins; TAF11, also called TATA Binding Protein (TBP) associated factor 11, TFIID subunit p30-beta, or transcription initiation factor TFIID 28 kDa subunit (TAF(II)28, TAFII-28, TAFII28), is a component of the TFIID complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors. TAF11 interacts with the ligand binding domains of the nuclear receptors for vitamin D3 and thyroid hormone. TAF11 also directly interacts with TFIIA, acting as a bridging factor that stabilizes the TFIIA-TBP-DNA complex.


Pssm-ID: 467028  Cd Length: 87  Bit Score: 56.40  E-value: 2.07e-11
                         10        20
                 ....*....|....*....|....
gi 394953994 113 FSEEQLNRYEMYRRSAFPKAAIKR 136
Cdd:cd08048    1 FTEEQLERYEAFRRSKFNKSAIKR 24
TAF40 COG5251
Transcription initiation factor TFIID, subunit TAF11 [Transcription];
99-136 6.62e-07

Transcription initiation factor TFIID, subunit TAF11 [Transcription];


Pssm-ID: 227576  Cd Length: 199  Bit Score: 46.96  E-value: 6.62e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 394953994  99 DEDEI---QKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKR 136
Cdd:COG5251   83 DENELaqdERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKK 123
 
Name Accession Description Interval E-value
TAFII28 pfam04719
hTAFII28-like protein conserved region; The general transcription factor, TFIID, consists of ...
 108-137 1.12e-14

hTAFII28-like protein conserved region; The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C-terminal of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3.


Pssm-ID: 428086  Cd Length: 86  Bit Score: 64.81  E-value: 1.12e-14
                          10        20        30
                  ....*....|....*....|....*....|
gi 394953994  108 ILVSSFSEEQLNRYEMYRRSAFPKAAIKRH 137
Cdd:pfam04719   1 LLLSNFSEEQLDRYEVFRRSSFNKAVIKKL 30
HFD_TAF11 cd08048
histone-fold domain found in transcription initiation factor TFIID subunit 11 (TAF11) and ...
 113-136 2.07e-11

histone-fold domain found in transcription initiation factor TFIID subunit 11 (TAF11) and similar proteins; TAF11, also called TATA Binding Protein (TBP) associated factor 11, TFIID subunit p30-beta, or transcription initiation factor TFIID 28 kDa subunit (TAF(II)28, TAFII-28, TAFII28), is a component of the TFIID complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors. TAF11 interacts with the ligand binding domains of the nuclear receptors for vitamin D3 and thyroid hormone. TAF11 also directly interacts with TFIIA, acting as a bridging factor that stabilizes the TFIIA-TBP-DNA complex.


Pssm-ID: 467028  Cd Length: 87  Bit Score: 56.40  E-value: 2.07e-11
                         10        20
                 ....*....|....*....|....
gi 394953994 113 FSEEQLNRYEMYRRSAFPKAAIKR 136
Cdd:cd08048    1 FTEEQLERYEAFRRSKFNKSAIKR 24
TAF40 COG5251
Transcription initiation factor TFIID, subunit TAF11 [Transcription];
99-136 6.62e-07

Transcription initiation factor TFIID, subunit TAF11 [Transcription];


Pssm-ID: 227576  Cd Length: 199  Bit Score: 46.96  E-value: 6.62e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 394953994  99 DEDEI---QKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKR 136
Cdd:COG5251   83 DENELaqdERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKK 123
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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