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0  structures 473  species 0  interactions 786  sequences 18  architectures

Family: TAF1_subA (PF14929)

Summary: TAF RNA Polymerase I subunit A

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This is the Wikipedia entry entitled "TBP-associated factor". More...

TBP-associated factor Edit Wikipedia article

TBP associated factor (TAF6)
PDB 1taf EBI.jpg
drosophila dtafii42/dtafii62 (like TAF6/TAF9) heterotetramer, HFD
Pfam clanCL0012

The TBP-associated factors (TAF) are proteins that associate with the TATA-binding protein in transcription initiation. It is a part of the transcription initiation factor TFIID multimeric protein complex. It also makes up many other factors, including SL1. They mediate the formation of the transcription preinitiation complex, a step preceding transcription of DNA to RNA by RNA polymerase II.

TAFs have a signature N-terminal histone-like fold domain (HFD).[1] This domain is implicated in the pairwise interaction among specific TAFs.[2]



TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFS).[3]

TAF is part of the TFIID complex, and interacts with the following:

  • Specific transcriptional activators
  • Basal transcription factors
  • Other TAFIIs
  • Specific DNA sequences, for example the downstream promoter element or gene-specific core promoter sequence

Due to such interactions, they contribute transcription activation and to promoter selectivity.[3]

Some pairs of TAF interact with each other to form "lobes" in TFIID. Pairs known or suggested to exist in TFIID include TAF6-TAF9, TAF4-TAF12, TAF11-13, TAF8-TAF10 and TAF3-TAF10.[2]


Selective factor 1 is composed of the TATA-binding protein and three TAF (TATA box-binding protein-associated factor) subunits (TAF1A, TAF1B, and TAF1C). These TAFs do not have a histone-like fold domain.[4]

Other complexes

TAF is a part of SAGA (SPT-ADA-GCN5 acetylase) and related coactivation complexes.[2] Such complexes acetylate histone tails to activate genes.[5] Human has three SAGA-like complexes: PCAF, TFTC (TBP-free TAF-containing complex), and STAGA (SPT3-TAF9-GCN5L acetylase). PCAF (GCN5) and KAT2A (GCN5L) are two human homologs of the yeast Gcn5.[6]

TAF8, TAF10, and SPT7L forms a small TAF complex called SMAT.[2]


The N-terminal domain of TAF has a histone-like protein fold. It contains two short alpha helices and a long central alpha helix.[1]

Human genes

Assorted signatures

TAF domains are spread out across many digital signatures:

TAF/Nervy homology (TAF4/4B)
TAF RNA Polymerase I subunit A (TAF1A)


  1. ^ a b Xie X, Kokubo T, Cohen SL, Mirza UA, Hoffmann A, Chait BT, Roeder RG, Nakatani Y, Burley SK (March 1996). "Structural similarity between TAFs and the heterotetrameric core of the histone octamer". Nature. 380 (6572): 316–22. Bibcode:1996Natur.380..316X. doi:10.1038/380316a0. PMID 8598927. S2CID 4329570.
  2. ^ a b c d Demény MA, Soutoglou E, Nagy Z, Scheer E, Jànoshàzi A, Richardot M, Argentini M, Kessler P, Tora L (March 2007). "Identification of a small TAF complex and its role in the assembly of TAF-containing complexes". PLOS ONE. 2 (3): e316. Bibcode:2007PLoSO...2..316D. doi:10.1371/journal.pone.0000316. PMC 1820849. PMID 17375202.
  3. ^ a b Furukawa T, Tanese N (September 2000). "Assembly of partial TFIID complexes in mammalian cells reveals distinct activities associated with individual TATA box-binding protein-associated factors". The Journal of Biological Chemistry. 275 (38): 29847–56. doi:10.1074/jbc.M002989200. PMID 10896937.
  4. ^ Friedrich JK, Panov KI, Cabart P, Russell J, Zomerdijk JC (August 2005). "TBP-TAF complex SL1 directs RNA polymerase I pre-initiation complex formation and stabilizes upstream binding factor at the rDNA promoter". The Journal of Biological Chemistry. 280 (33): 29551–8. doi:10.1074/jbc.M501595200. PMC 3858828. PMID 15970593.
  5. ^ Bonnet J, Wang CY, Baptista T, Vincent SD, Hsiao WC, Stierle M, Kao CF, Tora L, Devys D (September 2014). "The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription". Genes & Development. 28 (18): 1999–2012. doi:10.1101/gad.250225.114. PMC 4173158. PMID 25228644.
  6. ^ Martinez E, Palhan VB, Tjernberg A, Lymar ES, Gamper AM, Kundu TK, Chait BT, Roeder RG (October 2001). "Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo". Molecular and Cellular Biology. 21 (20): 6782–95. doi:10.1128/MCB.21.20.6782-6795.2001. PMC 99856. PMID 11564863.
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TAF RNA Polymerase I subunit A Provide feedback

TATA box binding protein associated factor RNA Polymerase I subunit A is found in eukaryotes and is encoded by the gene TAF1A in humans. Its function is to aid transcription of DNA into RNA by binding to the promoter at the -10 TATA box site. It is a component of the transcription factor SL1/TIF-IB complex, involved in PIC assembly (pre-initiation complex) during RNA polymerase I-dependent transcription. The rate of PIC formation depends on the rate of association of this protein. This protein also stabilises nucleolar transcription factor 1/UBTF on rDNA.

Literature references

  1. Comai L, Zomerdijk JC, Beckmann H, Zhou S, Admon A, Tjian R;, Science. 1994;266:1966-1972.: Reconstitution of transcription factor SL1: exclusive binding of TBP by SL1 or TFIID subunits. PUBMED:7801123 EPMC:7801123

This tab holds annotation information from the InterPro database.

InterPro entry IPR039495

TATA box binding protein associated factor RNA Polymerase I subunit A is found in eukaryotes and is encoded by the gene TAF1A in humans. Its function is to aid transcription of DNA into RNA by binding to the promoter at the -10 TATA box site. It is a component of the transcription factor SL1/TIF-IB complex, involved in PIC assembly (pre-initiation complex) during RNA polymerase I-dependent transcription. The rate of PIC formation depends on the rate of association of this protein. This protein also stabilises nucleolar transcription factor 1/UBTF on rDNA [ PUBMED:7801123 ].

This entry also includes TAF1A homologues from plants.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan TPR (CL0020), which has the following description:

Tetratricopeptide-like repeats are found in a numerous and diverse proteins involved in such functions as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.

The clan contains the following 252 members:

14-3-3 AAR2 Aconitase_B_N Adaptin_N Alkyl_sulf_dimr ANAPC3 ANAPC5 ANAPC8 Apc1_MidN APC_rep API5 Aquarius_N Arm Arm_2 Arm_3 Arm_vescicular Atx10homo_assoc B56 BAF250_C BRO1 BTAD CAS_CSE1 ChAPs CHIP_TPR_N CID CLASP_N Clathrin Clathrin-link Clathrin_H_link Clathrin_propel Cnd1 Cnd1_N Cnd3 CNOT1_CAF1_bind CNOT1_HEAT_N CNOT1_TTP_bind Coatomer_E Cohesin_HEAT Cohesin_load ComR_TPR COPI_C CPL CRM1_C CRM1_repeat CRM1_repeat_3 Cse1 CTK3 CTNNBL Cullin DHR-2_Lobe_A DHR-2_Lobe_C DIL DNA-PKcs_N DNA_alkylation DNAPKcs_CC1-2 DNAPKcs_CC3 DNAPKcs_CC5 Dopey_N Drf_FH3 Drf_GBD DUF1822 DUF2019 DUF2225 DUF3385 DUF3458_C DUF3730 DUF3856 DUF4042 DUF4704 DUF5071 DUF5106 DUF5588 DUF5691 DUF6340 DUF6377 DUF6584 DUF924 E_motif EAD11 eIF-3c_N ELMO_ARM EST1 EST1_DNA_bind FA_FANCE FANCF FANCI_HD1 FANCI_HD2 FANCI_S1 FANCI_S1-cap FANCI_S2 FANCI_S3 FANCI_S4 FAT Fes1 Fis1_TPR_C Fis1_TPR_N Focadhesin Foie-gras_1 GET4 GLE1 GUN4_N HAT HEAT HEAT_2 HEAT_EZ HEAT_PBS HEAT_UF HemY_N HMW1C_N HPS6_C HrpB1_HrpK HSM3_C HSM3_N Hyccin IBB IBN_N IFRD Iml2-TPR_39 Importin_rep Importin_rep_2 Importin_rep_3 Importin_rep_4 Importin_rep_5 Importin_rep_6 Insc_C Ints3_N KAP Kinetochor_Ybp2 Laa1_Sip1_HTR5 Leuk-A4-hydro_C LRV LRV_FeS MA3 Mad3_BUB1_I MAP3K_TRAF_bd MIF4G MIF4G_like MIF4G_like_2 MIX MMS19_C Mo25 MRP-S27 Mtf2 MUN NatA_aux_su Neurobeachin Neurochondrin Nic96 Nipped-B_C Not1 Nro1 NSF Paf67 ParcG PAT1 PC_rep PDS5 Peptidase_M9_N PHAT PI3Ka PknG_TPR PPP5 PPR PPR_1 PPR_2 PPR_3 PPR_long PPTA Proteasom_PSMB PUF PUL RAI16-like Rapsyn_N Rcd1 RIH_assoc RINT1_TIP1 RIX1 RNPP_C RPM2 RPN6_N RPN7 RYDR_ITPR Sel1 SHNi-TPR SIL1 SLT_L SNAP SPO22 SRP_TPR_like ST7 STAG Suf SusD-like SusD-like_2 SusD-like_3 SusD_RagB SYCP2_ARLD SYMPK_PTA1_N TAF1_subA TAF6_C TAL_effector TAP42 TAtT Tcf25 TIP120 TOM20_plant TPR-S TPR_1 TPR_10 TPR_11 TPR_12 TPR_14 TPR_15 TPR_16 TPR_17 TPR_18 TPR_19 TPR_2 TPR_20 TPR_21 TPR_22 TPR_3 TPR_4 TPR_5 TPR_6 TPR_7 TPR_8 TPR_9 TPR_MalT Tra1_ring TRF TTC7_N Type_III_YscG UNC45-central Upf2 Uso1_p115_head V-ATPase_H_C V-ATPase_H_N Vac14_Fab1_bd Vitellogenin_N Vps16_C Vps35 Vps39_1 VPS53_C W2 Wap1 WSLR Wzy_C_2 Xpo1 YcaO_C YfiO Zmiz1_N


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Curation and family details

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Curation View help on the curation process

Seed source: Jackhmmer: Q15573
Previous IDs: none
Type: Repeat
Sequence Ontology: SO:0001068
Author: Coggill P , Hetherington K
Number in seed: 34
Number in full: 786
Average length of the domain: 347.90 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 72.74 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 31.8 31.8
Trusted cut-off 31.9 32.5
Noise cut-off 31.7 31.6
Model length: 371
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;