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Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF TATA-BINDING PROTEIN

Authors :   B. S. Dedecker, P. B. Sigler

Date :   04 Oct 96 (Deposition) - 11 Jan 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Transcription Regulation, Dna-Binding Protein, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. S. Dedecker, R. O'Brien, P. J. Fleming, J. H. Geiger, S. P. Jackson, P. B. Sigler
The Crystal Structure Of A Hyperthermophilic Archaeal Tata-Box Binding Protein.
J. Mol. Biol. V. 264 1072 1996
PubMed-ID: 9000631 | Reference-DOI: 10.1006/JMBI.1996.0697
(for further references see the PDB file header)

Molecule 1 - TATA-BINDING PROTEIN
	Cell Line	:	BL21
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET 11A (NOVAGEN)
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET
	Organism Scientific	:	PYROCOCCUS WOESEI
	Organism Taxid	:	2262
	Synonym	:	TBP

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1PCZ)

Asymmetric/Biological Unit

No.	Residues
1	A:33	-	A:48
2	B:33	-	B:48

Asymmetric/Biological Unit

No.	Residues
1	Asp A:52	-	Pro A:53
2	Glu A:143	-	Pro A:144
3	Asp B:52	-	Pro B:53
4	Glu B:143	-	Pro B:144

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TFIID	PS00351	Transcription factor TFIID repeat signature.	TBP_PYRWO	38-87 129-178	4	A:38-87 B:38-87 A:129-178 B:129-178

(no "Exon" information available for 1PCZ)

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:183
 aligned with TBP_PYRWO | P62001 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181   
            TBP_PYRWO     2 VDMSKVKLRIENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGAKSVQDIERAVAKLAQKLKSIGVKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKYGLL 184
               SCOP domains d1pcza1 A:2-92 TATA-box binding protein (TBP), C-terminal domain                           d1pcza2 A:93-184 TATA-box binding protein (TBP), C-terminal domain                           SCOP domains
               CATH domains ---1pczA01    1pczA02 A:16-102 TATA-Binding Protein                                                  1pczA01 A:5-15,A:103-184 TATA-Binding Protein                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeeeeeeeeee......hhhhhhh.............eeeee....eeeee....eeeee....hhhhhhhhhhhhhhhhhh........eeee.eeeeeee......hhhhhhh...eeee...eeeeeeee....eeeee....eeeee....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------TFIID  PDB: A:38-87 UniProt: 38-87                -----------------------------------------TFIID  PDB: A:129-178 UniProt: 129-178            ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pcz A   2 VDMSKVKLRIENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGAKSVQDIERAVAKLAQKLKSIGVKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKYGLL 184
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain B from PDB  Type:PROTEIN  Length:183
 aligned with TBP_PYRWO | P62001 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181   
            TBP_PYRWO     2 VDMSKVKLRIENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGAKSVQDIERAVAKLAQKLKSIGVKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKYGLL 184
               SCOP domains d1pczb1 B:2-92 TATA-box binding protein (TBP), C-terminal domain                           d1pczb2 B:93-184 TATA-box binding protein (TBP), C-terminal domain                           SCOP domains
               CATH domains ---1pczB01    1pczB02 B:16-102 TATA-Binding Protein                                                  1pczB01 B:5-15,B:103-184 TATA-Binding Protein                                      CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------TBP-1pczB01 B:97-182                                                                  -- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------TBP-1pczB02 B:97-182                                                                  -- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------TBP-1pczB03 B:97-182                                                                  -- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------TBP-1pczB04 B:97-182                                                                  -- Pfam domains (4)
         Sec.struct. author ..hhh.eeeeeeeeeeee......hhhhhhh..eee........eeeee....eeeee....eeeee....hhhhhhhhhhhhhhhhhh........eeee.eeeeeee......hhhhhhh.............eeeee....eeeee....eeeee....hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------TFIID  PDB: B:38-87 UniProt: 38-87                -----------------------------------------TFIID  PDB: B:129-178 UniProt: 129-178            ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pcz B   2 VDMSKVKLRIENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGAKSVQDIERAVAKLAQKLKSIGVKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKYGLL 184
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

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)

Pyrococcus woesei [TaxId: 2262] (3)

1a	d1pcza1	A:2-92
1b	d1pcza2	A:93-184
1c	d1pczb1	B:2-92
1d	d1pczb2	B:93-184

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)

Pyrococcus woesei. Organism_taxid: 2262. Cell_line: bl21. (1)

1a	1pczA01	A:5-15,A:103-184
1b	1pczB01	B:5-15,B:103-184
1c	1pczA02	A:16-102
1d	1pczB02	B:16-102

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TBP-like (48)

Family: TBP (22)

Pyrococcus woesei (1)

1a	TBP-1pczB01	B:97-182
1b	TBP-1pczB02	B:97-182
1c	TBP-1pczB03	B:97-182
1d	TBP-1pczB04	B:97-182

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TBP_PYRWO | P62001)

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	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Asp A:52 - Pro A:53	[ RasMol ]
		Asp B:52 - Pro B:53	[ RasMol ]
		Glu A:143 - Pro A:144	[ RasMol ]
		Glu B:143 - Pro B:144	[ RasMol ]

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SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

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