1TBA - JenaLib

NMR Structure

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:67
 aligned with TAF1_DROME | P51123 from UniProtKB/Swiss-Prot  Length:2129

    Alignment length:67
                                    20        30        40        50        60        70       
           TAF1_DROME    11 EGSIGNGLDLTGILFGNIDSEGRLLQDDDGEGRGGTGFDAELRENIGSLSKLGLDSMLLEVIDLKEA  77
               SCOP domains d1tbaa_ A: TAF(II)230 TBP-binding fragment                          SCOP domains
               CATH domains 1tbaA00 A:11-77 Transcription Initiation Factor IId 230k Chain A    CATH domains
               Pfam domains TBP-binding-1tbaA01 A:11-77                                         Pfam domains
         Sec.struct. author ............hhhh..........................hhhhhh.....hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 1tba A  11 EGSIGNGLDLTGILFGNIDSEGRLLQDDDGEGRGGTGFDAELRENIGSLSKLGLDSMLLEVIDLKEA  77
                                    20        30        40        50        60        70

Chain B from PDB  Type:PROTEIN  Length:180
 aligned with TBP_YEAST | P13393 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:180
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
            TBP_YEAST    61 SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM 240
               SCOP domains d1tbab1 B:61-155 TATA-box binding protein (TBP), C-terminal domain                             d1tbab2 B:156-240 TATA-box binding protein (TBP), C-terminal domain                   SCOP domains
               CATH domains 1tbaB01    1tbaB02 B:72-157 TATA-Binding Protein                                                 1tbaB01 B:61-71,B:158-240 TATA-Binding Protein                                      CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------TBP-1tbaB01 B:152-238                                                                  -- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------TBP-1tbaB02 B:152-238                                                                  -- Pfam domains (2)
         Sec.struct. author .....eeeeeeeeee......hhhhhhh............eeeeee....eeeeee...eeeeeee..hhhhhhhhhhhhhhhhhh............eeeeeee......hhhhhhh..............eeeee....eeeee....eeeee....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------TFIID  PDB: B:94-143 UniProt: 94-143              -----------------------------------------TFIID  PDB: B:185-234 UniProt: 185-234            ------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:61-240 UniProt: 1-240 [INCOMPLETE]                                                                                                                                  Transcript 1
                 1tba B  61 SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM 240
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

NMR Structure(hide GO term definitions)

Chain A (TAF1_DROME | P51123)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0001129	RNA polymerase II transcription factor activity, TBP-class protein binding, involved in preinitiation complex assembly	Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), to facilitate the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.
	GO:0004402	histone acetyltransferase activity	Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0001075	transcription factor activity, RNA polymerase II core promoter sequence-specific binding involved in preinitiation complex assembly	Interacting selectively and non-covalently with a specific DNA sequence in an RNA polymerase II (Pol II) core promoter, the region composed of the transcription start site and binding sites for transcription factors of the Pol II basal transcription machinery, in order to promote assembly of the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase II promoter.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006352	DNA-templated transcription, initiation	Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	GO:0051123	RNA polymerase II transcriptional preinitiation complex assembly	The aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0016573	histone acetylation	The modification of a histone by the addition of an acetyl group.
	GO:0022008	neurogenesis	Generation of cells within the nervous system.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0060261	positive regulation of transcription initiation from RNA polymerase II promoter	Any process that increases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.
	GO:0007221	positive regulation of transcription of Notch receptor target	The activation of transcription of specific genes as a result of Notch signaling, mediated by the Notch intracellular domain.
	GO:0006461	protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0046425	regulation of JAK-STAT cascade	Any process that modulates the frequency, rate or extent of the JAK-STAT signaling pathway.
	GO:0051726	regulation of cell cycle	Any process that modulates the rate or extent of progression through the cell cycle.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006367	transcription initiation from RNA polymerase II promoter	Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005669	transcription factor TFIID complex	A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.

Chain B (TBP_YEAST | P13393)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008301	DNA binding, bending	The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
	GO:0001179	RNA polymerase I transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase I transcription factor, any protein required to initiate or regulate transcription by RNA polymerase I.
	GO:0001102	RNA polymerase II activating transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
	GO:0000979	RNA polymerase II core promoter sequence-specific DNA binding	Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.
	GO:0001016	RNA polymerase III regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that controls the transcription of a gene by RNA polymerase III. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	GO:0001026	TFIIIB-type transcription factor activity	Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, Once recruited to an RNA polymerase III promoter by one or more other transcription factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0001186	transcription factor activity, RNA polymerase I transcription factor recruiting	The function of binding to an RNA polymerase I (RNAP I) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP I.
	GO:0001075	transcription factor activity, RNA polymerase II core promoter sequence-specific binding involved in preinitiation complex assembly	Interacting selectively and non-covalently with a specific DNA sequence in an RNA polymerase II (Pol II) core promoter, the region composed of the transcription start site and binding sites for transcription factors of the Pol II basal transcription machinery, in order to promote assembly of the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase II promoter.
biological process
	GO:0006352	DNA-templated transcription, initiation	Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	GO:0051123	RNA polymerase II transcriptional preinitiation complex assembly	The aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.
	GO:0070898	RNA polymerase III transcriptional preinitiation complex assembly	The aggregation, arrangement and bonding together of proteins on promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase III promoter.
	GO:0006356	regulation of transcription from RNA polymerase I promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase I promoter.
	GO:0006359	regulation of transcription from RNA polymerase III promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA ploymerase III promoter.
	GO:0006385	transcription elongation from RNA polymerase III promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase III promoter by the addition of ribonucleotides catalyzed by RNA polymerase III.
	GO:0006383	transcription from RNA polymerase III promoter	The synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter.
	GO:0042790	transcription of nuclear large rRNA transcript from RNA polymerase I promoter	The synthesis of the large ribosomal RNA (rRNA) transcript which encodes several rRNAs, e.g. in mammals 28S, 18S and 5.8S, from a nuclear DNA template transcribed by RNA polymerase I.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0070893	transposon integration	Any process in which a transposable element is incorporated into another DNA molecule such as a chromosome.
cellular component
	GO:0070860	RNA polymerase I core factor complex	A RNA polymerase I-specific transcription factor complex that is required for the transcription of rDNA by RNA polymerase I. In yeast the complex consists of Rrn6p, Rrn7p, and Rrn11p.
	GO:0000500	RNA polymerase I upstream activating factor complex	A complex required for the transcription of rDNA by RNA polymerase I. In yeast the complex consists of Rrrn5p, Rrn9p, Rrn10p, histones H3 and H4, and Uaf30p.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005669	transcription factor TFIID complex	A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.
	GO:0000126	transcription factor TFIIIB complex	A transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIB contains the TATA-binding protein (TBP) and two Pol III-specific proteins, B'' and BRF.

Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 50)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (1, 1)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 3)

CATH Domains (2, 3)

Pfam Domains (2, 3)

Gene Ontology (52, 60)

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