1AIS | PDR031 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Authors :   P. F. Kosa, G. Ghosh, B. S. Dedecker, P. B. Sigler

Date :   24 Apr 97 (Deposition) - 07 Jul 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

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

Reference :   P. F. Kosa, G. Ghosh, B. S. Dedecker, P. B. Sigler
The 2. 1-A Crystal Structure Of An Archaeal Preinitiation Complex: Tata-Box-Binding Protein/Transcription Factor (Ii)B Core/Tata-Box.
Proc. Natl. Acad. Sci. Usa V. 94 6042 1997
PubMed-ID: 9177165 | Reference-DOI: 10.1073/PNAS.94.12.6042
(for further references see the PDB file header)

*Molecule 1 - DNA (5'-D(APAPCPTPTPAPCPTPTPTP(5IU) P(5IU)PAPAPAPGPC)-3')**
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - DNA (5'- D(GPCPTPTPTPAPAPAPAPAPGPTPAPAPGPTPT )-3')**
	Chains	:	E
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - PROTEIN (TATA-BINDING PROTEIN)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21
	Expression System Taxid	:	469008
	Expression System Variant	:	DE3
	Fragment	:	RESIDUES 1 - 181
	Organism Scientific	:	PYROCOCCUS WOESEI
	Organism Taxid	:	2262
	Synonym	:	TBP

Molecule 4 - PROTEIN (TRANSCRIPTION INITIATION FACTOR IIB)
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21
	Expression System Taxid	:	469008
	Expression System Variant	:	DE3
	Fragment	:	C TERMINAL DOMAIN
	Organism Scientific	:	PYROCOCCUS WOESEI
	Organism Taxid	:	2262
	Synonym	:	TFB TFIIB

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	5IU	2	Mod. Nucleotide	5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

(no "Site" information available for 1AIS)

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 1AIS)

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 1AIS)

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 d1aisa1 A:1-92 TATA-box binding protein (TBP), C-terminal domain                            d1aisa2 A:93-181 TATA-box binding protein (TBP), C-terminal domain                        SCOP domains
               CATH domains ----1aisA01    1aisA02 A:16-102 TATA-Binding Protein                                                  1aisA01 A:5-15,A:103-181 TATA-Binding Protein                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeee......hhhh................eeee......eeee....eeeee....hhhhhhhhhhhhhhhhhh........eeee.eeeeeee......hhhhhhh.............eeeee....eeeee....eeeeeee..hhhhhhhhhhhhhhh... 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
                1ais 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:193
 aligned with TF2B_PYRWO | P61999 from UniProtKB/Swiss-Prot  Length:300

    Alignment length:193
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297   
          TF2B_PYRWO    108 NLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVDKKEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTVRNRYKELVEKLKIKVPIA  300
               SCOP domains d1aisb1 B:1108-1205 Transcription factor IIB (TFIIB), core domain                                 d1aisb2 B:1206-1300 Transcription factor IIB (TFIIB), core domain                               SCOP domains
               CATH domains 1aisB01 B:1108-1206  [code=1.10.472.10, no name defined]                                           1aisB02 B:1207-1300  [code=1.10.472.10, no name defined]                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------TFIIB           ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------TFIIB           ----------------------------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ais B 1108 NLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIARVDKKEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTVRNRYKELVEKLKIKVPIA 1300
                                  1117      1127      1137      1147      1157      1167      1177      1187      1197      1207      1217      1227      1237      1247      1257      1267      1277      1287      1297

Chain C from PDB  Type:DNA  Length:17
                                                  
                1ais C 1401 AACTTACTTTuuAAAGC 1417
                                  1410||     
                                   1411-5IU  
                                    1412-5IU

Chain E from PDB  Type:DNA  Length:17
                                                  
                1ais E 1418 GCTTTAAAAAGTAAGTT 1434
                                  1427

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	1aisA01	A:5-15,A:103-181
1b	1aisA02	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	1aisB01	B:1108-1206
2b	1aisB02	B:1207-1300

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

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	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.

Chain B (TF2B_PYRWO | P61999)

molecular function
	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: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.
	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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		5IU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 1ais)

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1ais
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	TBP_PYRWO \| P62001
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	TF2B_PYRWO \| P61999
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	TBP_PYRWO \| P62001
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	TF2B_PYRWO \| P61999
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TBP_PYRWO \| P62001	:	1d3u 1pcz
	TF2B_PYRWO \| P61999	:	1d3u

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

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)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (8, 12)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File