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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TBX5 IN THE DNA-BOUND AND DNA-FREE FORM
 
Authors :  D. Ptchelkine, C. U. Stirnimann, C. Grimm, C. W. Mueller
Date :  22 Feb 10  (Deposition) - 28 Apr 10  (Release) - 24 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transcription-Dna Complex, Holt-Oram-Syndrome, Developmental Protein, Transcription Regulation, Repressor, Dna-Binding, Transcription, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. U. Stirnimann, D. Ptchelkine, C. Grimm, C. W. Muller
Structural Basis Of Tbx5-Dna Recognition: The T- Box Domain In Its Dna-Bound And -Unbound Form.
J. Mol. Biol. V. 400 71 2010
PubMed-ID: 20450920  |  Reference-DOI: 10.1016/J.JMB.2010.04.052

(-) Compounds

Molecule 1 - T-BOX TRANSCRIPTION FACTOR TBX5
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROX HTB
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: T-BOX DOMAIN, RESIDUES 51-251
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: T-BOX PROTEIN 5, HUMAN TBX5
 
Molecule 2 - 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP)-3'
    Chains: C
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - 5'-D(*TP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP)-3'
    Chains: D
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2PE41Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:60 , SER A:86 , LYS A:88BINDING SITE FOR RESIDUE MG A1239
2AC2SOFTWAREGLU B:60 , SER B:86BINDING SITE FOR RESIDUE MG B1233
3AC3SOFTWARELEU A:103 , ASP A:105 , ARG A:182 , ARG B:182 , PHE B:201BINDING SITE FOR RESIDUE PE4 B1234

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:202 -B:202

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly A:53 -Ile A:54
2Phe A:84 -Pro A:85
3Ser A:141 -Pro A:142
4Phe B:84 -Pro B:85
5Ser B:141 -Pro B:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 14)

Asymmetric/Biological Unit (8, 14)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_015382I54TTBX5_HUMANDisease (HOS)104894384A/BI54T
2UniProtVAR_009701G80RTBX5_HUMANDisease (HOS)104894381A/BG80R
3UniProtVAR_076673P132STBX5_HUMANDisease  ---A/BP132S
4UniProtVAR_074599A143TTBX5_HUMANDisease374906778A/BA143T
5UniProtVAR_074600S154ATBX5_HUMANDisease  ---A/BS154A
6UniProtVAR_076642H170DTBX5_HUMANDisease  ---A/BH170D
7UniProtVAR_007456R237QTBX5_HUMANDisease (HOS)104894378AR237Q
8UniProtVAR_009702R237WTBX5_HUMANDisease (HOS)104894382AR237W
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TBOX_3PS50252 T-box domain profile.TBX5_HUMAN58-238
 		  2A:58-238
B:58-232
2TBOX_1PS01283 T-box domain signature 1.TBX5_HUMAN63-82
 		  2A:63-82
B:63-82
3TBOX_2PS01264 T-box domain signature 2.TBX5_HUMAN137-155
 		  2A:137-155
B:137-155

(-) Exons   (0, 0)

(no "Exon" information available for 2X6V)

(-) 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:177
 aligned with TBX5_HUMAN | Q99593 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:186
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232      
           TBX5_HUMAN    53 GIKVFLHERELWLKFHEVGTEMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSVTGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRG 238
               SCOP domains d2x6va_ A: automated matches                                                                                                                                                               SCOP domains
               CATH domains 2x6vA00 A:53-238  [code=2.60.40.820, no name defined]                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhh.eee.....ee.....eeeee......eeeeeeeeee...eeeeee..eeeeeee.........ee.....eehhhhhhh.ee....eee.........ee.....eeeeeeeee...---------.eeeeee.hhhheeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) -T-------------------------R---------------------------------------------------S----------T----------A---------------D------------------------------------------------------------------Q- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W- SAPs(SNPs) (2)
                PROSITE (1) -----TBOX_3  PDB: A:58-238 UniProt: 58-238                                                                                                                                                 PROSITE (1)
                PROSITE (2) ----------TBOX_1  PDB: A:63-82------------------------------------------------------TBOX_2             ----------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x6v A  53 GIKVFLHERELWLKFHEVGTEMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSVTGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKAD---------TAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRG 238
                                    62        72        82        92       102       112       122       132       142       152       162       172       182      |  -      |202       212       222       232      
                                                                                                                                                                  189       199                                       


Chain B from PDB  Type:PROTEIN  Length:172
 aligned with TBX5_HUMAN | Q99593 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:181
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 
           TBX5_HUMAN    52 EGIKVFLHERELWLKFHEVGTEMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSVTGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPF 232
               SCOP domains d2x6vb_ B: automated matches                                                                                                                                                          SCOP domains
               CATH domains 2x6vB00 B:52-232  [code=2.60.40.820, no name defined]                                                                                                                                 CATH domains
           Pfam domains (1) ---T-box-2x6vB01 B:55-232                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) ---T-box-2x6vB02 B:55-232                                                                                                                                                             Pfam domains (2)
         Sec.struct. author ...eeee.hhhhhhhhhhhh.eee.....ee.....eeeee......eeeeeeeeee...eeeee....eeeeee.........ee.....eehhhhhhh.ee....eee.........ee.....eeeeeeeeee..---------.eeeee.hhhhheeee....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --T-------------------------R---------------------------------------------------S----------T----------A---------------D-------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------TBOX_3  PDB: B:58-232 UniProt: 58-238                                                                                                                                           PROSITE (1)
                PROSITE (2) -----------TBOX_1  PDB: B:63-82------------------------------------------------------TBOX_2             ----------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x6v B  52 EGIKVFLHERELWLKFHEVGTEMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSVTGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKAD---------TAFCTHVFPETAFIAVTSYQNHKITQLKIENNPF 232
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       | -       201       211       221       231 
                                                                                                                                                                   189       199                                 


Chain C from PDB  Type:DNA  Length:11
                                           
                 2x6v C   1 TCTCACACCTT  11
                                    10 


Chain D from PDB  Type:DNA  Length:11
                                           
                 2x6v D  12 TAAGGTGTGAG  22
                                    21
   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  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TBX5_HUMAN | Q99593)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    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).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0001228    transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
    GO:0003283    atrial septum development    The progression of the atrial septum over time, from its initial formation to the mature structure.
    GO:0060413    atrial septum morphogenesis    The developmental process in which atrial septum is generated and organized. The atrial septum separates the upper chambers (the atria) of the heart from one another.
    GO:0003181    atrioventricular valve morphogenesis    The process in which the structure of the atrioventricular valve is generated and organized.
    GO:0003166    bundle of His development    The process whose specific outcome is the progression of the bundle of His over time, from its formation to the mature structure. The bundle of His is part of the His-Purkinje system that transmits signals from the AV node to the cardiac Purkinje fibers.
    GO:0003218    cardiac left ventricle formation    The developmental process pertaining to the initial formation of a left cardiac ventricle from unspecified parts.
    GO:0055007    cardiac muscle cell differentiation    The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
    GO:0060980    cell migration involved in coronary vasculogenesis    The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form the blood vessels of the heart.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0035115    embryonic forelimb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human.
    GO:0030326    embryonic limb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping.
    GO:0003197    endocardial cushion development    The progression of a cardiac cushion over time, from its initial formation to the mature structure. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.
    GO:0035136    forelimb morphogenesis    The process in which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0002009    morphogenesis of an epithelium    The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
    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:0060044    negative regulation of cardiac muscle cell proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle cell proliferation.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0010719    negative regulation of epithelial to mesenchymal transition    Any process that decreases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
    GO:0007389    pattern specification process    Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.
    GO:0060039    pericardium development    The process whose specific outcome is the progression of the pericardium over time, from its formation to the mature structure. The pericardium is a double-walled sac that contains the heart and the roots of the aorta, vena cava and the pulmonary artery.
    GO:0060045    positive regulation of cardiac muscle cell proliferation    Any process that activates or increases the frequency, rate or extent of cardiac muscle cell proliferation.
    GO:0051891    positive regulation of cardioblast differentiation    Any process that activates or increases the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating.
    GO:0072513    positive regulation of secondary heart field cardioblast proliferation    Any process that activates or increases the frequency, rate or extent of cardioblast proliferation in the second heart field. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating. The secondary heart field is the region of the heart that will form the majority of the mesodermal component of the right ventricle, the arterial pole (outflow tract) and the venous pole (inflow tract).
    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:1900117    regulation of execution phase of apoptosis    Any process that modulates the frequency, rate or extent of execution phase of apoptosis.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II 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. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0060290    transdifferentiation    The conversion of a differentiated cell of one fate into a differentiated cell of another fate without first undergoing cell division or reversion to a more primitive or stem cell-like fate.
    GO:0003229    ventricular cardiac muscle tissue development    The process whose specific outcome is the progression of ventricular cardiac muscle over time, from its formation to the mature structure.
    GO:0003281    ventricular septum development    The progression of the ventricular septum over time from its formation to the mature structure.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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  2x6v
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  TBX5_HUMAN | Q99593
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 Related Entries

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

UniProtKB/Swiss-Prot
        TBX5_HUMAN | Q99593: 2x6u 4s0h 5bqd

(-) Related Entries Specified in the PDB File

2x6u CRYSTAL STRUCTURE OF HUMAN TBX5 IN THE DNA -FREE FORM