Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE T(-27) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.
 
Authors :  G. A. Patikoglou, J. L. Kim, L. Sun, S. -H. Yang, T. Kodadek, S. K. Burley
Date :  14 Oct 99  (Deposition) - 07 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Tata Box-Binding Protein (Tbp), Adenovirus Major Late Promoter (Admlp) Tata Box, Tbp-Tata Element Complexes, T (- 27) Tata Box Variant (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. A. Patikoglou, J. L. Kim, L. Sun, S. -H. Yang, T. Kodadek, S. K. Burley
Tata Element Recognition By The Tata Box-Binding Protein Has Been Conserved Throughout Evolution
Genes Dev. V. 13 3217 1999
PubMed-ID: 10617571  |  Reference-DOI: 10.1101/GAD.13.24.3217

(-) Compounds

Molecule 1 - TRANSCRIPTION INITIATION FACTOR TFIID-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: TATA-BOX FACTOR 1, TATA SEQUENCE-BINDING PROTEIN 1, TBP1
 
Molecule 2 - DNA (5'-D(*GP*CP*TP*AP*TP*AP*TP*AP*AP*GP*GP*GP*CP*A)-3')
    Chains: C, E
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*AP*TP*AP*TP*AP*GP*C)-3')
    Chains: D, F
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1QN7)

(-) Sites  (0, 0)

(no "Site" information available for 1QN7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QN7)

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QN7)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TFIIDPS00351 Transcription factor TFIID repeat signature.TBP1_ARATH52-101
 
143-192
 		  4A:52-101
B:52-101
A:143-192
B:143-192
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TFIIDPS00351 Transcription factor TFIID repeat signature.TBP1_ARATH52-101
 
143-192
 		  2A:52-101
-
A:143-192
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TFIIDPS00351 Transcription factor TFIID repeat signature.TBP1_ARATH52-101
 
143-192
 		  2-
B:52-101
-
B:143-192

(-) Exons   (0, 0)

(no "Exon" information available for 1QN7)

(-) Sequences/Alignments

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:186
 aligned with TBP1_ARATH | P28147 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:186
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192      
           TBP1_ARATH    13 DLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI 198
               SCOP domains d1qn7a1 A:13-115 TATA-box binding protein (TBP), C-terminal domain                                     d1qn7a2 A:116-198 TATA-box binding protein (TBP), C-terminal domain                 SCOP domains
               CATH domains ------1qn7A01    1qn7A02 A:30-115 TATA-Binding Protein                                                 1qn7A01 A:19-29,A:116-197 TATA-Binding Protein                                    - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeeeeeee.....hhhhhhhhh..eee.......eeeee....eeeee....eeeee...hhhhhhhhhhhhhhhhhh.............eeeeeee.....hhhhhhhhh.............eeeee....eeeee....eeeeeee.hhhhhhhhhhhhhhhhhhh... 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
                 1qn7 A  13 DLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI 198
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192      


Chain B from PDB  Type:PROTEIN  Length:186
 aligned with TBP1_ARATH | P28147 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:186
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191      
           TBP1_ARATH    12 VDLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRK 197
               SCOP domains d1qn7b1 B:12-115 TATA-box binding protein (TBP), C-terminal domain                                      d1qn7b2 B:116-197 TATA-box binding protein (TBP), C-terminal domain                SCOP domains
               CATH domains -------1qn7B01    1qn7B02 B:30-115 TATA-Binding Protein                                                 1qn7B01 B:19-29,B:116-197 TATA-Binding Protein                                     CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------TBP-1qn7B01 B:110-196                                                                  - Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------TBP-1qn7B02 B:110-196                                                                  - Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------TBP-1qn7B03 B:110-196                                                                  - Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------TBP-1qn7B04 B:110-196                                                                  - Pfam domains (4)
         Sec.struct. author ............eeeeeeeeee.....hhhhhhhhh...........eeeeee....eeeeee...eeeee...hhhhhhhhhhhhhhhhhhh............eeeeeee.....hhhhhhhhh.............eeeee....eeeee....eeeeeee.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
                 1qn7 B  12 VDLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRK 197
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191      


Chain C from PDB  Type:DNA  Length:14
                                              
                 1qn7 C 201 GCTATATAAGGGCA 214
                                   210    


Chain D from PDB  Type:DNA  Length:14
                                              
                 1qn7 D 215 TGCCCTTATATAGC 228
                                   224    


Chain E from PDB  Type:DNA  Length:14
                                              
                 1qn7 E 201 GCTATATAAGGGCA 214
                                   210    


Chain F from PDB  Type:DNA  Length:14
                                              
                 1qn7 F 215 TGCCCTTATATAGC 228
                                   224
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: TBP-like (48)
(-)
Family: TBP (22)
(-)
Arabidopsis thaliana (Mouse-ear cress) (10)
1aTBP-1qn7B01B:110-196
1bTBP-1qn7B02B:110-196
1cTBP-1qn7B03B:110-196
1dTBP-1qn7B04B:110-196

(-) Gene Ontology  (6, 6)

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.

 Visualization

(-) Interactive Views

Asymmetric 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
(no "Ligands, Modified Residues, Ions" information available for 1qn7)
 
  Sites
(no "Sites" information available for 1qn7)
 
  Cis Peptide Bonds
    Glu A:66 - Pro A:67   [ RasMol ]  
    Glu B:66 - Pro B:67   [ RasMol ]  
    Val A:157 - Pro A:158   [ RasMol ]  
    Val B:157 - Pro B:158   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1qn7
    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
  TBP1_ARATH | P28147
    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

(-) Analysis Tools

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
  TBP1_ARATH | P28147
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TBP1_ARATH | P28147: 1qn3 1qn4 1qn5 1qn6 1qn8 1qn9 1qna 1qnb 1qnc 1qne 1vok 1vol 1vtl 1vto pdt009 pdt025

(-) Related Entries Specified in the PDB File

1qn3 CRYSTAL STRUCTURE OF THE C(-25) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.
1qn4 CRYSTAL STRUCTURE OF THE T(-24) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.
1qn5 CRYSTAL STRUCTURE OF THE G(-26) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.
1qn6 CRYSTAL STRUCTURE OF THE T(-26) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.
1qn8 CRYSTAL STRUCTURE OF THE T(-28) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.
1qn9 CRYSTAL STRUCTURE OF THE C(-29) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.
1qna CRYSTAL STRUCTURE OF THE T(-30) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.
1qnb CRYSTAL STRUCTURE OF THE T(-25) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.
1qnc CRYSTAL STRUCTURE OF THE A(-31) ADENOVIRUS MAJOR LATE PROMOTER TATA BOX VARIANT BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2). TATA ELEMENT RECOGNITION BY THE TATA BOX-BINDING PROTEIN HAS BEEN CONSERVED THROUGHOUT EVOLUTION.
1qne CRYSTAL STRUCTURE OF THE ADENOVIRUS MAJOR LATE PROMOTER TATA BOX BOUND TO WILD-TYPE TBP (ARABIDOPSIS THALIANA TBP ISOFORM 2).