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 :  CO-CRYSTAL STRUCTURE OF TBP RECOGNIZING THE MINOR GROOVE OF A TATA ELEMENT
 
Authors :  J. L. Kim, D. B. Nikolov, S. K. Burley
Date :  17 Dec 93  (Deposition) - 13 Jul 11  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Protein-Dna Complex, Double Helix, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Kim, D. B. Nikolov, S. K. Burley
Co-Crystal Structure Of Tbp Recognizing The Minor Groove Of A Tata Element
Nature V. 365 520 1993
PubMed-ID: 8413605  |  Reference-DOI: 10.1038/365520A0

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
    Chains: A, C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')
    Chains: B, D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - TATA BINDING PROTEIN (TBP)
    Chains: E, F
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1VTL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VTL)

(-) 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:DNA  Length:14
                                              
                 1vtl A 201 GCTATAAAAGGGCA 214
                                   210    


Chain B from PDB  Type:DNA  Length:14
                                              
                 1vtl B 301 TGCCCTTTTATAGC 314
                                   310    


Chain C from PDB  Type:DNA  Length:14
                                              
                 1vtl C 401 GCTATAAAAGGGCA 414
                                   410    


Chain D from PDB  Type:DNA  Length:14
                                              
                 1vtl D 501 TGCCCTTTTATAGC 514
                                   510    


Chain E 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 d1vtle1 E:13-106 automated matches                                                            d1vtle2 E:107-198 automated matches                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeeeeeee.....hhhhhhhhh..ee........eeeee....eeeee....eeeeeee.hhhhhhhhhhhhhhhhhh.......eeeeeeeeeeeee.....hhhhhhhhh...ee........eeeee....eeeee....eeeeeee.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------TFIID  PDB: E:52-101 UniProt: 52-101              -----------------------------------------TFIID  PDB: E:143-192 UniProt: 143-192            ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vtl E  13 DLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI 198
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192      


Chain F 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 d1vtlf1 F:13-106 automated matches                                                            d1vtlf2 F:107-198 automated matches                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeeeeeee.....hhhhhhhhh...ee.......eeeee....eeeee....eeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeee.....hhhhhhhhh...ee........eeee......eeee....eeeeeee.hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------TFIID  PDB: F:52-101 UniProt: 52-101              -----------------------------------------TFIID  PDB: F:143-192 UniProt: 143-192            ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vtl F  13 DLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI 198
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192
   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  (0, 0)

(no "CATH Domain" information available for 1VTL)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain E,F   (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 1vtl)
 
  Sites
(no "Sites" information available for 1vtl)
 
  Cis Peptide Bonds
    Glu E:66 - Pro E:67   [ RasMol ]  
    Glu F:66 - Pro F:67   [ RasMol ]  
    Val E:157 - Pro E:158   [ RasMol ]  
    Val F:157 - Pro F: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
  1vtl
    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 1qn7 1qn8 1qn9 1qna 1qnb 1qnc 1qne 1vok 1vol 1vto pdt009 pdt025

(-) Related Entries Specified in the PDB File

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