1MP9 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

Title :   TBP FROM A MESOTHERMOPHILIC ARCHAEON, SULFOLOBUS ACIDOCALDARIUS

Authors :   H. Koike, Y. Kawashima-Ohya, T. Yamasaki, L. Clowney, Y. Katsuya, M. Suzuki

Date :   12 Sep 02 (Deposition) - 04 Nov 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   H. Koike, Y. Kawashima-Ohya, T. Yamasaki, L. Clowney, Y. Katsuya, M. Suzuki
Origins Of Protein Stability Revealed By Comparing Crystal Structures Of Tata Binding Proteins.
Structure V. 12 157 2004
PubMed-ID: 14725775 | Reference-DOI: 10.1016/J.STR.2003.12.003
(for further references see the PDB file header)

Molecule 1 - TATA-BINDING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET21B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	SULFOLOBUS ACIDOCALDARIUS
	Organism Taxid	:	2285
	Synonym	:	BOX A BINDING PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1MP9)

(no "Site" information available for 1MP9)

(no "SS Bond" information available for 1MP9)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:56	-	Pro A:57
2	Glu A:147	-	Pro A:148
3	Ser B:56	-	Pro B:57
4	Glu B:147	-	Pro B:148

(no "SAP(SNP)/Variant" information available for 1MP9)

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_SULAC	41-90 132-181	4	A:42-91 B:42-91 A:133-182 B:133-182

(no "Exon" information available for 1MP9)

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:193
 aligned with TBP_SULAC | Q9UWN7 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:193
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193   
            TBP_SULAC     4 DEIPYKAVVNIENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGAKSTDELIKAVKRIIKTLKKYGMQLTGKPKIQIQNIVASANLHVIVNLDKAAFLLENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIFDKLVELDCVKPVEEEELE 196
               SCOP domains d1mp9a1 A:5-96 TATA-box binding protein (TBP), C-terminal domain                            d1mp9a2 A:97-197 TATA-box binding protein (TBP), C-terminal domain                                    SCOP domains
               CATH domains ----1mp9A01    1mp9A02 A:20-106 TATA-Binding Protein                                                  1mp9A01 A:9-19,A:107-191 TATA-Binding Protein                                        ------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeee.....hhhhhhhhh............eeeee....eeeee....eeeee...hhhhhhhhhhhhhhhhhhh........eeeeeeeeeeee...eehhhhhhhhh..ee........eeeee....eeeee....eeeeeee.hhhhhhhhhhhhhhhhhhh..ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------TFIID  PDB: A:42-91 UniProt: 41-90                -----------------------------------------TFIID  PDB: A:133-182 UniProt: 132-181            --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mp9 A   5 DEIPYKAVVNIENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGAKSTDELIKAVKRIIKTLKKYGMQLTGKPKIQIQNIVASANLHVIVNLDKAAFLLENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIFDKLVELDCVKPVEEEELE 197
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194

Chain B from PDB  Type:PROTEIN  Length:189
 aligned with TBP_SULAC | Q9UWN7 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:189
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181         
            TBP_SULAC     2 IPDEIPYKAVVNIENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGAKSTDELIKAVKRIIKTLKKYGMQLTGKPKIQIQNIVASANLHVIVNLDKAAFLLENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIFDKLVELDCVKPV 190
               SCOP domains d1mp9b1 B:3-96 TATA-box binding protein (TBP), C-terminal domain                              d1mp9b2 B:97-191 TATA-box binding protein (TBP), C-terminal domain                              SCOP domains
               CATH domains ------1mp9B01    1mp9B02 B:20-106 TATA-Binding Protein                                                  1mp9B01 B:9-19,B:107-191 TATA-Binding Protein                                         CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------TBP-1mp9B01 B:101-186                                                                 ----- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------TBP-1mp9B02 B:101-186                                                                 ----- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------TBP-1mp9B03 B:101-186                                                                 ----- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------TBP-1mp9B04 B:101-186                                                                 ----- Pfam domains (4)
         Sec.struct. author .........eeeeeeeeeeee.....hhhhhhhhh............eeeee....eeeee....eeeee...hhhhhhhhhhhhhhhhhhh........eeeeeeeeeeee..eeehhhhhhhhh..ee........eeeee....eeeee....eeeeeee.hhhhhhhhhhhhhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------TFIID  PDB: B:42-91 UniProt: 41-90                -----------------------------------------TFIID  PDB: B:133-182 UniProt: 132-181            --------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mp9 B   3 IPDEIPYKAVVNIENIVATVTLDQTLDLYAMERSVPNVEYDPDQFPGLIFRLESPKITSLIFKSGKMVVTGAKSTDELIKAVKRIIKTLKKYGMQLTGKPKIQIQNIVASANLHVIVNLDKAAFLLENNMYEPEQFPGLIYRMDEPRVVLLIFSSGKMVITGAKREDEVHKAVKKIFDKLVELDCVKPV 191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

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)

Sulfolobus acidocaldarius [TaxId: 2285] (1)

1a	d1mp9a1	A:5-96
1b	d1mp9a2	A:97-197
1c	d1mp9b1	B:3-96
1d	d1mp9b2	B:97-191

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)

Sulfolobus acidocaldarius. Organism_taxid: 2285. (1)

1a	1mp9A01	A:9-19,A:107-191
1b	1mp9B01	B:9-19,B:107-191
1c	1mp9A02	A:20-106
1d	1mp9B02	B:20-106

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TBP-like (48)

Family: TBP (22)

Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (1)

1a	TBP-1mp9B01	B:101-186
1b	TBP-1mp9B02	B:101-186
1c	TBP-1mp9B03	B:101-186
1d	TBP-1mp9B04	B:101-186

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TBP_SULAC | Q9UWN7)

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
		Glu A:147 - Pro A:148	[ RasMol ]
		Glu B:147 - Pro B:148	[ RasMol ]
		Ser A:56 - Pro A:57	[ RasMol ]
		Ser B:56 - Pro B:57	[ RasMol ]

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	1mp9
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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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