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(-) Description

Title :  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.
 
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 :  1.90
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, C (- 29) 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*CP*AP*AP*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*TP*TP*GP*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 1QN9)

(-) Sites  (0, 0)

(no "Site" information available for 1QN9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QN9)

(-) 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 1QN9)

(-) 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 1QN9)

(-) 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:183
 aligned with TBP1_ARATH | P28147 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:183
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195   
           TBP1_ARATH    16 KHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI 198
               SCOP domains d1qn9a1 A:16-115 TATA-box binding protein (TBP), C-terminal domain                                  d1qn9a2 A:116-198 TATA-box binding protein (TBP), C-terminal domain                 SCOP domains
               CATH domains ---1qn9A01    1qn9A02 A:30-115 TATA-Binding Protein                                                 1qn9A01 A:19-29,A:116-197 TATA-Binding Protein                                    - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee.....hhhhhhhhh..eee.......eeeee....eeeee....eeeeeee.hhhhhhhhhhhhhhhhhhh............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
                 1qn9 A  16 KHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI 198
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195   


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 d1qn9b1 B:12-115 TATA-box binding protein (TBP), C-terminal domain                                      d1qn9b2 B:116-197 TATA-box binding protein (TBP), C-terminal domain                SCOP domains
               CATH domains -------1qn9B01    1qn9B02 B:30-115 TATA-Binding Protein                                                 1qn9B01 B:19-29,B:116-197 TATA-Binding Protein                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeeeeeeee.....hhhhhhhhh...........eeeeee....eeeeee...eeeeeee.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
                 1qn9 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
                                              
                 1qn9 C 201 GCTACAAAAGGGCA 214
                                   210    


Chain D from PDB  Type:DNA  Length:14
                                              
                 1qn9 D 215 TGCCCTTTTGTAGC 228
                                   224    


Chain E from PDB  Type:DNA  Length:14
                                              
                 1qn9 E 201 GCTACAAAAGGGCA 214
                                   210    


Chain F from PDB  Type:DNA  Length:14
                                              
                 1qn9 F 215 TGCCCTTTTGTAGC 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  (0, 0)

(no "Pfam Domain" information available for 1QN9)

(-) 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.

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  Cis Peptide Bonds
    Glu A:66 - Pro A:67   [ RasMol ]  
    Glu B:66 - Pro B:67   [ RasMol ]  
    Val A:157 - Pro A:158   [ RasMol ]  
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  1qn9
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 Related Entries

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

UniProtKB/Swiss-Prot
        TBP1_ARATH | P28147: 1qn3 1qn4 1qn5 1qn6 1qn7 1qn8 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.
1qn7 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.
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.
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).