1CDW | PDT034 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   HUMAN TBP CORE DOMAIN COMPLEXED WITH DNA

Authors :   D. B. Nikolov, H. Chen, E. D. Halay, A. Hoffmann, R. G. Roeder, S. K. Burley

Date :   11 Apr 96 (Deposition) - 23 Dec 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B,C

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

Reference :   D. B. Nikolov, H. Chen, E. D. Halay, A. Hoffman, R. G. Roeder, S. K. Burley
Crystal Structure Of A Human Tata Box-Binding Protein/Tata Element Complex.
Proc. Natl. Acad. Sci. Usa V. 93 4862 1996
PubMed-ID: 8643494 | Reference-DOI: 10.1073/PNAS.93.10.4862
(for further references see the PDB file header)

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

*Molecule 2 - DNA (5'- D(CPAPGPCPCPTPTPTPTPAPTPAPGPCPAPG)-3')*
	Chains	:	C
	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	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1CDW)

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

Asymmetric/Biological Unit

No.	Residues
1	Glu A:202	-	Pro A:203
2	Lys A:293	-	Pro A:294

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

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_HUMAN	192-241 283-332	2	A:188-237 A:279-328

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000392092	1b	ENSE00001510680	chr6:170863459-170863551	93	TBP_HUMAN	-	0	0	-	-
1.3b	ENST00000392092	3b	ENSE00001510679	chr6:170865970-170866171	202	TBP_HUMAN	1-18	18	0	-	-
1.4c	ENST00000392092	4c	ENSE00000854357	chr6:170870879-170871321	443	TBP_HUMAN	19-166	148	1	A:155-162	8
1.5	ENST00000392092	5	ENSE00000766152	chr6:170873633-170873720	88	TBP_HUMAN	166-195	30	1	A:162-191	30
1.6b	ENST00000392092	6b	ENSE00000766154	chr6:170876006-170876097	92	TBP_HUMAN	196-226	31	1	A:192-222	31
1.7b	ENST00000392092	7b	ENSE00001593404	chr6:170878700-170878867	168	TBP_HUMAN	226-282	57	1	A:222-278	57
1.8	ENST00000392092	8	ENSE00001773146	chr6:170880498-170880592	95	TBP_HUMAN	282-314	33	1	A:278-310	33
1.9b	ENST00000392092	9b	ENSE00001510678	chr6:170881274-170881944	671	TBP_HUMAN	314-339	26	1	A:310-333	24

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:179
 aligned with TBP_HUMAN | P20226 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:179
                                   168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328         
            TBP_HUMAN   159 SGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 337
               SCOP domains d1cdwa1 A:155-252 TATA-box binding protein (TBP), C-terminal domain                               d1cdwa2 A:253-333 TATA-box binding protein (TBP), C-terminal domain               SCOP domains
               CATH domains 1cdwA01    1cdwA02 A:166-251 TATA-Binding Protein                                                1cdwA01 A:155-165,A:252-333 TATA-Binding Protein                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee......hhhhhhh...eee......eeeeee....eeeeee...eeeeeee..hhhhhhhhhhhhhhhhhh............eeeeeee......hhhhhhh..............eeeee....eeeee....eeeee....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------TFIID  PDB: A:188-237 UniProt: 192-241            -----------------------------------------TFIID  PDB: A:279-328 UniProt: 283-332            ----- PROSITE
           Transcript 1 (1) 1.4c    -----------------------------Exon 1.6b  PDB: A:192-222      -------------------------------------------------------Exon 1.8  PDB: A:278-310         ----------------------- Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.5  PDB: A:162-191      ------------------------------Exon 1.7b  PDB: A:222-278 UniProt: 226-282               -------------------------------Exon 1.9b  PDB: A:310-33 Transcript 1 (2)
                 1cdw A 155 SGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEENSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRK 333
                                   164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324

Chain B from PDB  Type:DNA  Length:16
                                                
                 1cdw B   1 CTGCTATAAAAGGCTG  16
                                    10

Chain C from PDB  Type:DNA  Length:16
                                                
                 1cdw C 101 CAGCCTTTTATAGCAG 116
                                   110

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: TBP-like (289)

Superfamily: TATA-box binding protein-like (70)

Family: TATA-box binding protein (TBP), C-terminal domain (29)

Protein domain: TATA-box binding protein (TBP), C-terminal domain (29)

Human (Homo sapiens) [TaxId: 9606] (5)

1a	d1cdwa1	A:155-252
1b	d1cdwa2	A:253-333

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	1cdwA01	A:155-165,A:252-333
1b	1cdwA02	A:166-251

(no "Pfam Domain" information available for 1CDW)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TBP_HUMAN | P20226)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003700	DNA-binding transcription factor activity	A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
	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:0000978	RNA polymerase II proximal promoter sequence-specific DNA binding	Interacting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in the proximal promoter of a gene transcribed by RNA polymerase II. The proximal promoter is in cis with and relatively close to the core promoter.
	GO:0001103	RNA polymerase II repressing transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	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:0070491	repressing transcription factor binding	Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
	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.
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:0045815	positive regulation of gene expression, epigenetic	Any epigenetic process that activates or increases the rate of gene expression.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:1901796	regulation of signal transduction by p53 class mediator	Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0042795	snRNA transcription by RNA polymerase II	The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	GO:0006363	termination of RNA polymerase I transcription	The process in which the synthesis of an RNA molecule by RNA polymerase I using a DNA template is completed. RNAP I termination requires binding of a terminator protein so specific sequences downstream of the transcription unit.
	GO:0006366	transcription by RNA polymerase II	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	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:0006362	transcription elongation from RNA polymerase I promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I.
	GO:0006368	transcription elongation from RNA polymerase II promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
	GO:0006361	transcription initiation from RNA polymerase I promoter	Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an RNA polymerase I 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: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.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0001939	female pronucleus	The pronucleus originating from the ovum that is being fertilized.
	GO:0001940	male pronucleus	The pronucleus originating from the spermatozoa that was involved in fertilization.
	GO:0005719	nuclear euchromatin	The dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, a some being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin.
	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:0045120	pronucleus	The nucleus of either the ovum or the spermatozoon following fertilization. Thus, in the fertilized ovum, there are two pronuclei, one originating from the ovum, the other from the spermatozoon that brought about fertilization; they approach each other, but do not fuse until just before the first cleavage, when each pronucleus loses its membrane to release its contents.
	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).
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:202 - Pro A:203	[ RasMol ]
		Lys A:293 - Pro A:294	[ RasMol ]

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	1cdw
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Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (6, 6)

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