1VOK - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 6 (Jmol Viewer)

Title :   ARABIDOPSIS THALIANA TBP (DIMER)

Authors :   D. B. Nikolov, S. K. Burley

Date :   29 Apr 96 (Deposition) - 08 Nov 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (2x)
Biol. Unit 4: A,B  (2x)
Biol. Unit 5: A,B  (1x)
Biol. Unit 6: A  (2x)

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

Reference :   D. B. Nikolov, S. K. Burley
2. 1 A Resolution Refined Structure Of A Tata Box-Binding Protein (Tbp).
Nat. Struct. Biol. V. 1 621 1994
PubMed-ID: 7634102 | Reference-DOI: 10.1038/NSB0994-621
(for further references see the PDB file header)

Molecule 1 - TATA-BOX-BINDING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (2x)	:	A	B
Biological Unit 4 (2x)	:	A	B
Biological Unit 5 (1x)	:	A	B
Biological Unit 6 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 5 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 6 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE B:64 , ARG B:65 , GLU B:66 , LYS B:96 , HOH B:1279 , HOH B:1281 , HOH B:1282	BINDING SITE FOR RESIDUE SO4 B 2001

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

Asymmetric Unit

No.	Residues
1	Glu A:66	-	Pro A:67
2	Val A:157	-	Pro A:158
3	Glu B:66	-	Pro B:67
4	Val B:157	-	Pro B:158

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TFIID	PS00351	Transcription factor TFIID repeat signature.	TBP1_ARATH	52-101 143-192	4	A:52-101 B:52-101 A:143-192 B:143-192

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TFIID	PS00351	Transcription factor TFIID repeat signature.	TBP1_ARATH	52-101 143-192	2	A:52-101 - A:143-192 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TFIID	PS00351	Transcription factor TFIID repeat signature.	TBP1_ARATH	52-101 143-192	2	- B:52-101 - B:143-192

Biological Unit 3 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TFIID	PS00351	Transcription factor TFIID repeat signature.	TBP1_ARATH	52-101 143-192	8	A:52-101 B:52-101 A:143-192 B:143-192

Biological Unit 4 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TFIID	PS00351	Transcription factor TFIID repeat signature.	TBP1_ARATH	52-101 143-192	8	A:52-101 B:52-101 A:143-192 B:143-192

Biological Unit 5 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TFIID	PS00351	Transcription factor TFIID repeat signature.	TBP1_ARATH	52-101 143-192	4	A:52-101 B:52-101 A:143-192 B:143-192

Biological Unit 6 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TFIID	PS00351	Transcription factor TFIID repeat signature.	TBP1_ARATH	52-101 143-192	4	A:52-101 - A:143-192 -

(no "Exon" information available for 1VOK)

Asymmetric 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:192
 aligned with TBP1_ARATH | P28147 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:192
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196  
           TBP1_ARATH     7 EGSNPVDLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI 198
               SCOP domains d1voka1 A:7-115 TATA-box binding protein (TBP), C-terminal domain                                            d1voka2 A:116-198 TATA-box binding protein (TBP), C-terminal domain                 SCOP domains
               CATH domains ------------1vokA01    1vokA02 A:30-115 TATA-Binding Protein                                                 1vokA01 A:19-29,A:116-197 TATA-Binding Protein                                    - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................eeeeeeeeee......hhhhhhh.............eeeee....eeeee....eeeeeee..hhhhhhhhhhhhhhhhhh............eeeeeee......hhhhhhhh...eee.......eeeee....eeeee....eeeeeee..hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------TFIID  PDB: A:52-101 UniProt: 52-101              -----------------------------------------TFIID  PDB: A:143-192 UniProt: 143-192            ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vok A   7 EGSNPVDLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI 198
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196

Chain B from PDB  Type:PROTEIN  Length:188
 aligned with TBP1_ARATH | P28147 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:188
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
           TBP1_ARATH    12 VDLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKIQ 199
               SCOP domains d1vokb1 B:12-115 TATA-box binding protein (TBP), C-terminal domain                                      d1vokb2 B:116-199 TATA-box binding protein (TBP), C-terminal domain                  SCOP domains
               CATH domains -------1vokB01    1vokB02 B:30-115 TATA-Binding Protein                                                 1vokB01 B:19-29,B:116-198 TATA-Binding Protein                                     - CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------TBP-1vokB01 B:110-196                                                                  --- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------TBP-1vokB02 B:110-196                                                                  --- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------TBP-1vokB03 B:110-196                                                                  --- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------TBP-1vokB04 B:110-196                                                                  --- Pfam domains (4)
         Sec.struct. author ............eeeeeeeeee......hhhhhhh...eeee...eeeeeeee....eeeee....eeeeeee..hhhhhhhhhhhhhhhhh.............eeeeeee......hhhhhhhh...eee.......eeeee....eeeee....eeeee....hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------TFIID  PDB: B:52-101 UniProt: 52-101              -----------------------------------------TFIID  PDB: B:143-192 UniProt: 143-192            ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vok B  12 VDLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKIQ 199
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

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 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)

Thale cress (Arabidopsis thaliana) [TaxId: 3702] (13)

1a	d1voka1	A:7-115
1b	d1voka2	A:116-198
1c	d1vokb1	B:12-115
1d	d1vokb2	B:116-199

Asymmetric 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)

Thale cress (Arabidopsis thaliana) (1)

1a	1vokA01	A:19-29,A:116-197
1b	1vokB01	B:19-29,B:116-198
1c	1vokA02	A:30-115
1d	1vokB02	B:30-115

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TBP-like (48)

Family: TBP (22)

Arabidopsis thaliana (Mouse-ear cress) (10)

1a	TBP-1vokB01	B:110-196
1b	TBP-1vokB02	B:110-196
1c	TBP-1vokB03	B:110-196
1d	TBP-1vokB04	B:110-196

Asymmetric Unit(hide GO term definitions)

Chain A,B (TBP1_ARATH | P28147)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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.
cellular component
	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.

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		Val B:157 - Pro B:158	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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