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

(-) Description

Title :  T DOMAIN FROM XENOPUS LAEVIS BOUND TO DNA
 
Authors :  C. W. Muller
Date :  16 Jul 97  (Deposition) - 16 Jan 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Complex (Transcription Factor/Dna), Transcription Factor, Dna-Binding Protein, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. W. Muller, B. G. Herrmann
Crystallographic Structure Of The T Domain-Dna Complex Of The Brachyury Transcription Factor.
Nature V. 389 884 1997
PubMed-ID: 9349824  |  Reference-DOI: 10.1038/39929
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*G P*TP*GP*AP*AP*AP* TP*T)-3')
    Chains: C, D
    Engineered: YES
    Other Details: PALINDROMIC BINDING SITE OF THE T DOMAIN FROM AN IN VITRO SELECTION EXPERIMENT
 
Molecule 2 - PROTEIN (T PROTEIN)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Cellular Location: CYTOSOL
    Expression System Plasmid: PT7-7 (NOVAGEN)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Gene: XBRA
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Other Details: EUKARYOTIC TRANSCRIPTION FACTOR, TRANSIENTLY EXPRESSED IN THE EMBRYO, REQUIRED FOR MESODERM FORMATION
    Tissue: EMBRYO

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1XBR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:70 -Pro A:71
2Ser A:127 -Pro A:128
3Phe B:70 -Pro B:71
4Ser B:127 -Pro B:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TBOX_3PS50252 T-box domain profile.BRAC_XENLA44-217
 		  2A:44-217
B:44-217
2TBOX_1PS01283 T-box domain signature 1.BRAC_XENLA49-68
 		  2A:49-68
B:49-68
3TBOX_2PS01264 T-box domain signature 2.BRAC_XENLA123-141
 		  2A:123-141
B:123-141

(-) Exons   (0, 0)

(no "Exon" information available for 1XBR)

(-) Sequences/Alignments

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:184
 aligned with BRAC_XENLA | P24781 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:184
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218    
           BRAC_XENLA    39 ELKVSLEERDLWTRFKELTNEMIVTKNGRRMFPVLKVSMSGLDPNAMYTVLLDFVAADNHRWKYVNGEWVPGGKPEPQAPSCVYIHPDSPNFGAHWMKDPVSFSKVKLTNKMNGGGQIMLNSLHKYEPRIHIVRVGGTQRMITSHSFPETQFIAVTAYQNEEITALKIKHNPFAKAFLDAKERN 222
               SCOP domains d1xbra_ A: T domain from Brachyury transcription factor                                                                                                                                  SCOP domains
               CATH domains 1xbrA00 A:39-222  [code=2.60.40.820, no name defined]                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..hhhhhhhhhh..eee.............eeee......eeeeeeeeee....eeeee..eeeee....................hhhhhh...........................eeeeeeeeee......eeeee.hhh..eee.....hhhhhhhhhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----TBOX_3  PDB: A:44-217 UniProt: 44-217                                                                                                                                         ----- PROSITE (1)
                PROSITE (2) ----------TBOX_1  PDB: A:49-68------------------------------------------------------TBOX_2             --------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xbr A  39 ELKVSLEERDLWTRFKELTNEMIVTKNGRRMFPVLKVSMSGLDPNAMYTVLLDFVAADNHRWKYVNGEWVPGGKPEPQAPSCVYIHPDSPNFGAHWMKDPVSFSKVKLTNKMNGGGQIMLNSLHKYEPRIHIVRVGGTQRMITSHSFPETQFIAVTAYQNEEITALKIKHNPFAKAFLDAKERN 222
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218    


Chain B from PDB  Type:PROTEIN  Length:183
 aligned with BRAC_XENLA | P24781 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:183
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218   
           BRAC_XENLA    39 ELKVSLEERDLWTRFKELTNEMIVTKNGRRMFPVLKVSMSGLDPNAMYTVLLDFVAADNHRWKYVNGEWVPGGKPEPQAPSCVYIHPDSPNFGAHWMKDPVSFSKVKLTNKMNGGGQIMLNSLHKYEPRIHIVRVGGTQRMITSHSFPETQFIAVTAYQNEEITALKIKHNPFAKAFLDAKER 221
               SCOP domains d1xbrb_ B: T domain from Brachyury transcription factor                                                                                                                                 SCOP domains
               CATH domains 1xbrB00 B:39-221  [code=2.60.40.820, no name defined]                                                                                                                                   CATH domains
           Pfam domains (1) --T-box-1xbrB01 B:41-218                                                                                                                                                            --- Pfam domains (1)
           Pfam domains (2) --T-box-1xbrB02 B:41-218                                                                                                                                                            --- Pfam domains (2)
         Sec.struct. author ..eeee..hhhhhhhhhh..eee.............eeee.......eeeeeeeee....eeeee..eeeee....................hhhhhh...........................eeeeeeeee........eeee.hhh..eee.....hhhhhhhhhh.hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----TBOX_3  PDB: B:44-217 UniProt: 44-217                                                                                                                                         ---- PROSITE (1)
                PROSITE (2) ----------TBOX_1  PDB: B:49-68------------------------------------------------------TBOX_2             -------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xbr B  39 ELKVSLEERDLWTRFKELTNEMIVTKNGRRMFPVLKVSMSGLDPNAMYTVLLDFVAADNHRWKYVNGEWVPGGKPEPQAPSCVYIHPDSPNFGAHWMKDPVSFSKVKLTNKMNGGGQIMLNSLHKYEPRIHIVRVGGTQRMITSHSFPETQFIAVTAYQNEEITALKIKHNPFAKAFLDAKER 221
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218   


Chain C from PDB  Type:DNA  Length:24
                                                        
                 1xbr C 501 AATTTCACACCTAGGTGTGAAATT 524
                                   510       520    


Chain D from PDB  Type:DNA  Length:24
                                                        
                 1xbr D 501 AATTTCACACCTAGGTGTGAAATT 524
                                   510       520
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: P53-like (54)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BRAC_XENLA | P24781)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001102    RNA polymerase II activating transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
    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:0044344    cellular response to fibroblast growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an fibroblast growth factor stimulus.
    GO:0007368    determination of left/right symmetry    The establishment of an organism's body plan or part of an organism with respect to the left and right halves. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry.
    GO:0000578    embryonic axis specification    The establishment, maintenance and elaboration of a pattern along a line or a point in an embryo.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated 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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