1D3U | PD0070 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

Title :   TATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/BRE+TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI

Authors :   O. Littlefield, Y. Korkhin, P. B. Sigler

Date :   01 Oct 99 (Deposition) - 15 Nov 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

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

Reference :   O. Littlefield, Y. Korkhin, P. B. Sigler
The Structural Basis For The Oriented Assembly Of A Tbp/Tfb/Promoter Complex.
Proc. Natl. Acad. Sci. Usa V. 96 13668 1999
PubMed-ID: 10570130 | Reference-DOI: 10.1073/PNAS.96.24.13668
(for further references see the PDB file header)

Molecule 1
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - TATA-BINDING PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-180
	Organism Scientific	:	PYROCOCCUS WOESEI
	Organism Taxid	:	2262
	Synonym	:	TATA-BOX FACTOR, TATA SEQUENCE-BINDING PROTEIN, TBP

Molecule 4 - TRANSCRIPTION INITIATION FACTOR IIB
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL CORE, RESIDUES 62-261
	Organism Scientific	:	PYROCOCCUS WOESEI
	Organism Taxid	:	2262
	Synonym	:	TFIIB

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1D3U)

(no "Site" information available for 1D3U)

Asymmetric/Biological Unit

No.	Residues
1	A:33	-	A:48

Asymmetric/Biological Unit

No.	Residues
1	Glu A:143	-	Pro A:144

(no "SAP(SNP)/Variant" information available for 1D3U)

Asymmetric/Biological Unit (2, 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	2	A:38-87 A:129-178
2	TFIIB	PS00782	Transcription factor TFIIB repeat signature.	TF2B_PYRWO	148-163 244-259	2	B:1148-1163 B:1244-1259

(no "Exon" information available for 1D3U)

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:181
 aligned with TBP_PYRWO | P62001 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
           TBP_PYRWO      1 MVDMSKVKLRIENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGAKSVQDIERAVAKLAQKLKSIGVKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKY  181
               SCOP domains d1d3ua1 A:1-92 TATA-box binding protein (TBP), C-terminal domain                            d1d3ua2 A:93-181 TATA-box binding protein (TBP), C-terminal domain                        SCOP domains
               CATH domains ----1d3uA01    1d3uA02 A:16-102 TATA-Binding Protein                                                  1d3uA01 A:5-15,A:103-181 TATA-Binding Protein                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeee................eeee...eeeeeee......eeee....eeeeeee............................eeeeeeeeeeee................ee........eeeee....eeeee....eeeeeee.................... 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
                1d3u A    1 MVDMSKVKLRIENIVASVDLFAQLDLEKVLDLCPNSKYNPEEFPGIICHLDDPKVALLIFSSGKLVVTGAKSVQDIERAVAKLAQKLKSIGVKFKRAPQIDVQNMVFSGDIGREFNLDVVALTLPNCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSEADAWEAVRKLLRELDKY  181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:201
 aligned with TF2B_PYRWO | P61999 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:201
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299 
          TF2B_PYRWO    100 RVSDAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVDKKEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTVRNRYKELVEKLKIKVPIA  300
               SCOP domains d1d3ub1 B:1100-1205 Transcription factor IIB (TFIIB), core domain                                         d1d3ub2 B:1206-1300 Transcription factor IIB (TFIIB), core domain                               SCOP domains
               CATH domains --------1d3uB01 B:1108-1206  [code=1.10.472.10, no name defined]                                           1d3uB02 B:1207-1300  [code=1.10.472.10, no name defined]                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------TFIIB           ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------------------TFIIB           ----------------------------------------- PROSITE (1)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1d3u B 1100 MVSDAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVDKKEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTVRNRYKELVEKLKIKVPIA 1300
                                  1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299

Chain C from PDB  Type:DNA  Length:24
                                                         
                1d3u C 1401 AGAGTAAAGTTTAAATACTTATAT 1424
                                  1410      1420

Chain D from PDB  Type:DNA  Length:23
                                                        
                1d3u D 1426 TATAAGTATTTAAACTTTACTCT 1448
                                  1435      1445

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	1d3uA01	A:5-15,A:103-181
1b	1d3uA02	A:16-102

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cyclin A; domain 1 (136)

Homologous Superfamily: [code=1.10.472.10, no name defined] (99)

[unclassified] (5)

2a	1d3uB01	B:1108-1206
2b	1d3uB02	B:1207-1300

(no "Pfam Domain" information available for 1D3U)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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	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.
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.

Chain B (TF2B_PYRWO | P61999)

molecular function
	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: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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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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	Sites
(no "Sites" information available for 1d3u)

	Cis Peptide Bonds
		Glu A:143 - Pro A:144	[ RasMol ]

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	TBP_PYRWO \| P62001
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	TF2B_PYRWO \| P61999
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	TBP_PYRWO \| P62001
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UniProtKB/Swiss-Prot
	TBP_PYRWO \| P62001	:	1ais 1pcz
	TF2B_PYRWO \| P61999	:	1ais

(no "Related Entries Specified in the PDB File" available for 1D3U)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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SCOP Domains (2, 4)

CATH Domains (2, 4)

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Gene Ontology (8, 12)

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