1YTF | PDT036 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   YEAST TFIIA/TBP/DNA COMPLEX

Authors :   S. Tan, Y. Hunziker, D. F. Sargent, T. J. Richmond

Date :   05 Apr 96 (Deposition) - 20 Jun 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Transcription Regulation, Dna, Complex, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Tan, Y. Hunziker, D. F. Sargent, T. J. Richmond
Crystal Structure Of A Yeast Tfiia/Tbp/Dna Complex.
Nature V. 381 127 1996
PubMed-ID: 8610010 | Reference-DOI: 10.1038/381127A0
(for further references see the PDB file header)

*Molecule 1 - DNA (5'- D(TPGPTPAPTPGPTPAPTPAPTPAPAPAPAPC)-3')*
	Chains	:	E
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - DNA (5'- D(GPTPTPTPTPAPTPAPTPAPCPAPTPAPCPA)-3')*
	Chains	:	F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - PROTEIN (TATA BINDING PROTEIN (TBP))
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 4 - PROTEIN (TRANSCRIPTION FACTOR IIA - TOA1N SUBUNIT)
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Other Details	:	RECONSTITUTED FROM 3 INDIVIDUALLY OVEREXPRESSED POLYPEPTIDES

Molecule 5 - PROTEIN (TRANSCRIPTION FACTOR IIA - TOA1C SUBUNIT)
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 6 - PROTEIN (TRANSCRIPTION FACTOR IIA - TOA2 SUBUNIT)
	Chains	:	D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1YTF)

(no "Site" information available for 1YTF)

(no "SS Bond" information available for 1YTF)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:108	-	Pro A:109

(no "SAP(SNP)/Variant" information available for 1YTF)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TFIID	PS00351	Transcription factor TFIID repeat signature.	TBP_YEAST	94-143 185-234	2	A:94-143 A:185-234

Asymmetric/Biological Unit (3, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YER148W	1	YER148W.1	V:465298-466020	723	TBP_YEAST	1-240	240	1	A:61-240	180

2.1	YKL058W	1	YKL058W.1	XI:329810-330178	369	T2AG_YEAST	1-122	122	1	D:5-119 (gaps)	115

3.1	YOR194C	1	YOR194C.1	XV:712544-711684	861	TOA1_YEAST	1-286	286	2	B:2-47 C:241-286	46 46

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A 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 d1ytfa1 A:61-155 TATA-box binding protein (TBP), C-terminal domain                             d1ytfa2 A:156-240 TATA-box binding protein (TBP), C-terminal domain                   SCOP domains
               CATH domains 1ytfA01    1ytfA02 A:72-157 TATA-Binding Protein                                                 1ytfA01 A:61-71,A:158-240 TATA-Binding Protein                                      CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------TBP-1ytfA01 A:152-238                                                                  -- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------TBP-1ytfA02 A:152-238                                                                  -- Pfam domains (2)
         Sec.struct. author .....eeeeeeeeee......hhhhhhh...eee.......eeeee....eeeee....eeeee....hhhhhhhhhhhhhhhhhh............eeeeeee......hhhhhhh..............eeeee....eeeee....eeeee....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------TFIID  PDB: A:94-143 UniProt: 94-143              -----------------------------------------TFIID  PDB: A:185-234 UniProt: 185-234            ------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:61-240 UniProt: 1-240 [INCOMPLETE]                                                                                                                                  Transcript 1
                 1ytf A  61 SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM 240
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain B from PDB  Type:PROTEIN  Length:46
 aligned with TOA1_YEAST | P32773 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:46
                                    11        21        31        41      
           TOA1_YEAST     2 SNAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLT  47
               SCOP domains d1ytfb_ B: Large chain TOA1, N-terminal domain SCOP domains
               CATH domains 1ytfB00 B:2-47                                 CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
               Transcript 3 Exon 3.1  PDB: B:2-47 UniProt: 1-286           Transcript 3
                 1ytf B   2 SNAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLT  47
                                    11        21        31        41

Chain C from PDB  Type:PROTEIN  Length:46
 aligned with TOA1_YEAST | P32773 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:46
                                   250       260       270       280      
           TOA1_YEAST   241 ENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEWV 286
               SCOP domains d1ytfc_ C: Large chain TOA1, C-terminal domain SCOP domains
               CATH domains 1ytfC00 C:241-286                              CATH domains
           Pfam domains (1) TFIIA-1ytfC01 C:241-285                      - Pfam domains (1)
           Pfam domains (2) TFIIA-1ytfC02 C:241-285                      - Pfam domains (2)
         Sec.struct. author ..eeeeeeeeeeee..eeeeeee.eeeee..eeeee.eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
               Transcript 3 Exon 3.1  PDB: C:241-286 UniProt: 1-286        Transcript 3
                 1ytf C 241 ENLMLCLYDKVTRTKARWKCSLKDGVVTINRNDYTFQKAQVEAEWV 286
                                   250       260       270       280

Chain D from PDB  Type:PROTEIN  Length:100
 aligned with T2AG_YEAST | P32774 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:115
                                    14        24        34        44        54        64        74        84        94       104       114     
           T2AG_YEAST     5 GYYELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLTVKGNLDTYGFCDDVWTFIVKNCQVTVEDSHRDASQNGSGDSQSVISVDKLRIVACNSK 119
               SCOP domains d1ytfd1 D:5-54 Small chain TOA2, N-terminal domaind1ytfd2 D:55-119 Small chain TOA2,                C-terminal doma SCOP domains
               CATH domains 1ytfD01 D:5-57  [code=1.10.287.190, no name defined] 1ytfD02 D:58-119 TATA box bindi               ng Protein, subu CATH domains
               Pfam domains TFIIA_gamma_N-1ytfD02 D:5-53                     -TFIIA_gamma_C-1ytfD01 D:55-118                                  - Pfam domains
         Sec.struct. author ....hhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....eeeeeeeeeeeeee..eeeeeee.eeeee.---------------.eeee.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: D:5-119 (gaps) UniProt: 1-122 [INCOMPLETE]                                                           Transcript 2
                 1ytf D   5 GYYELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLTVKGNLDTYGFCDDVWTFIVKNCQVTVE---------------SVISVDKLRIVACNSK 119
                                    14        24        34        44        54        64        74        84   |     -       104       114     
                                                                                                              88             104

Chain E from PDB  Type:DNA  Length:16
                                                
                 1ytf E   1 TGTATGTATATAAAAC  16
                                    10

Chain F from PDB  Type:DNA  Length:16
                                                
                 1ytf F   1 GTTTTATATACATACA  16
                                    10

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: TATA-Binding Protein (118)

Homologous Superfamily: TATA-Binding Protein (37)

[unclassified] (13)

1a	1ytfA01	A:61-71,A:158-240
1b	1ytfA02	A:72-157

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: [code=1.10.287.100, no name defined] (9)

[unclassified] (4)

1ytfB00

B:2-47

Homologous Superfamily: [code=1.10.287.190, no name defined] (4)

[unclassified] (4)

1ytfD01

D:5-57

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: TATA box binding Protein, subunit D; domain 2 (4)

Homologous Superfamily: TATA box binding Protein, subunit D, domain 2 (4)

[unclassified] (4)

4a	1ytfD02	D:58-119
4b	1ytfC00	C:241-286

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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:0001186	RNA polymerase I transcription regulator recruiting activity	The function of binding to an RNA polymerase I (RNAP I) transcription regulator and recruiting it to the general transcription machinery complex in order to modulate transcription initiation.
	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 a DNA sequence that is part of the core promoter of a RNA polymerase II-transcribed gene.
	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: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:0001026	obsolete TFIIIB-type transcription factor activity	OBSOLETE. 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: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: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 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 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:0042790	nucleolar large rRNA transcription by RNA polymerase I	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:0006356	regulation of transcription by RNA polymerase I	Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase I.
	GO:0006359	regulation of transcription by RNA polymerase III	Any process that modulates the frequency, rate or extent of transcription mediated by RNA ploymerase III.
	GO:0006383	transcription by RNA polymerase III	The synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP 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: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.

Chain B,C (TOA1_YEAST | P32773)

molecular function
	GO:0017025	TBP-class protein binding	Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs).
	GO:0001129	obsolete RNA polymerase II transcription factor activity, TBP-class protein binding, involved in preinitiation complex assembly	OBSOLETE. 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: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:0003713	transcription coactivator activity	A protein or a member of a complex that interacts specifically and non-covalently with a DNA-bound DNA-binding transcription factor to activate the transcription of specific genes. Coactivators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second ATP-dependent class modifies the conformation of chromatin. Another type of coregulator activity is the bridging of a DNA-binding transcription factor to the basal transcription machinery. The Mediator complex, which bridges transcription factors and RNA polymerase, is also a transcription coactivator.
biological process
	GO:0051123	RNA polymerase II 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:1903506	regulation of nucleic acid-templated transcription	Any process that modulates the frequency, rate or extent of nucleic acid-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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005672	transcription factor TFIIA complex	A component of the transcription machinery of RNA Polymerase II. In humans, TFIIA is a heterotrimer composed of an alpha (P35), beta (P19) and gamma subunits (P12).

Chain D (T2AG_YEAST | P32774)

molecular function
	GO:0017025	TBP-class protein binding	Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs).
	GO:0001132	obsolete RNA polymerase II transcription factor activity, TBP-class protein binding	OBSOLETE. Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
	GO:0001129	obsolete RNA polymerase II transcription factor activity, TBP-class protein binding, involved in preinitiation complex assembly	OBSOLETE. 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: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).
biological process
	GO:0051123	RNA polymerase II 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:0006357	regulation of transcription by RNA polymerase II	Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase II.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005672	transcription factor TFIIA complex	A component of the transcription machinery of RNA Polymerase II. In humans, TFIIA is a heterotrimer composed of an alpha (P35), beta (P19) and gamma subunits (P12).

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1ytf)

	Sites
(no "Sites" information available for 1ytf)

	Cis Peptide Bonds
		Glu A:108 - Pro A:109	[ RasMol ]

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	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)
Insightii
	protein: ribbon, secondary structure; DNA: ribbon, sticks [ mono GIF format \| stereo GIF format ]
	protein: ribbon, secondary structure; DNA: spacefill [ mono GIF format \| stereo GIF format ]
	protein: ribbon, sticks; DNA: spacefill [ mono GIF format \| stereo GIF format ]
Midas
	protein: ribbon, secondary structure; DNA: ribbon, plates [ mono GIF format \| stereo GIF format ]
Setor
	protein: ribbon; DNA: ribbon, sticks [ mono GIF format \| stereo GIF format ]
	protein: ribbon; DBNA: spacefill ono, stereo) [ mono GIF format \| stereo GIF format ]
	protein: ribbon, sticks; DNA: spacefill [ mono GIF format \| stereo GIF format ]
Distance Plot
	representative atoms: CA, O3' [ mono GIF format \| mono PDF format ]

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	1ytf
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
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Access by UniProt ID/Accession number
	T2AG_YEAST \| P32774
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	TBP_YEAST \| P13393
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	TOA1_YEAST \| P32773
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

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	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	T2AG_YEAST \| P32774
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	TBP_YEAST \| P13393
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	TOA1_YEAST \| P32773
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	T2AG_YEAST \| P32774	:	1nh2 1rm1 5fmf 5fyw 5fz5 5sva
	TBP_YEAST \| P13393	:	1ngm 1nh2 1rm1 1tba 1tbp 1ytb 4b0a 4v1n 4v1o 5fmf 5fyw 5fz5 5sva
	TOA1_YEAST \| P32773	:	1nh2 1rm1 5fmf 5fyw 5fz5 5sva

(no "Related Entries Specified in the PDB File" available for 1YTF)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (3, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (5, 6)

CATH Domains (4, 6)

Pfam Domains (4, 6)

Gene Ontology (37, 50)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File