2X6U - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF HUMAN TBX5 IN THE DNA-FREE FORM

Authors :   C. U. Stirnimann, C. W. Mueller

Date :   22 Feb 10 (Deposition) - 28 Apr 10 (Release) - 24 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Developmental Protein, Dna-Binding, Holt-Oram-Syndrome, Ig-Fold, Nuclear Protein, Repressor, Tbx3, Transcription, Transcription Regulation (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

Molecule 1 - T-BOX TRANSCRIPTION FACTOR TBX5
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-M11
	Expression System Strain	:	BL21(DE3) RIPL
	Expression System Taxid	:	469008
	Fragment	:	T-BOX DOMAIN, RESIDUES 51-251
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HUMAN TBX5, T-BOX PROTEIN 5, TBX5

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION
2	PE4	1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:203 , HIS A:204 , VAL A:205 , PHE A:206 , HOH A:2134	BINDING SITE FOR RESIDUE PE4 A1231
2	AC2	SOFTWARE	LYS A:78 , LYS A:126 , ASN A:162	BINDING SITE FOR RESIDUE MG A1232
3	AC3	SOFTWARE	HIS A:112 , GLY A:125 , ASN A:162 , HOH A:2059	BINDING SITE FOR RESIDUE MG A1233
4	AC4	SOFTWARE	ARG A:81 , ARG A:82	BINDING SITE FOR RESIDUE MG A1234

(no "SS Bond" information available for 2X6U)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:84	-	Pro A:85
2	Ser A:141	-	Pro A:142

Asymmetric/Biological Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_015382	I	54	T	TBX5_HUMAN	Disease (HOS)	104894384	A	I	54	T
2	UniProt	VAR_009701	G	80	R	TBX5_HUMAN	Disease (HOS)	104894381	A	G	80	R
3	UniProt	VAR_074599	A	143	T	TBX5_HUMAN	Disease	374906778	A	A	143	T
4	UniProt	VAR_074600	S	154	A	TBX5_HUMAN	Disease	---	A	S	154	A
5	UniProt	VAR_076642	H	170	D	TBX5_HUMAN	Disease	---	A	H	170	D

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TBOX_3	PS50252	T-box domain profile.	TBX5_HUMAN	58-238	1	A:58-230
2	TBOX_1	PS01283	T-box domain signature 1.	TBX5_HUMAN	63-82	1	A:63-82
3	TBOX_2	PS01264	T-box domain signature 2.	TBX5_HUMAN	137-155	1	A:137-155

(no "Exon" information available for 2X6U)

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:176
 aligned with TBX5_HUMAN | Q99593 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:179
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221         
           TBX5_HUMAN    52 EGIKVFLHERELWLKFHEVGTEMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSVTGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENN 230
               SCOP domains d2x6ua_ A: automated matches                                                                                                                                                        SCOP domains
               CATH domains 2x6uA00 A:52-230  [code=2.60.40.820, no name defined]                                                                                                                               CATH domains
               Pfam domains ---T-box-2x6uA01 A:55-230                                                                                                                                                           Pfam domains
         Sec.struct. author ...eeee.hhhhhhhhhhhh.eee.....ee.....eeeee......eeeeeeeeeeeeeeeeeee..eeeeeee....---..ee.....eehhhhhhh.ee....eee.........ee....eeeeeeeeeee.............eeee.hhhhheeee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --T-------------------------R--------------------------------------------------------------T----------A---------------D------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------TBOX_3  PDB: A:58-230 UniProt: 58-238                                                                                                                                         PROSITE (1)
                PROSITE (2) -----------TBOX_1  PDB: A:63-82------------------------------------------------------TBOX_2             --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x6u A  52 EGIKVFLHERELWLKFHEVGTEMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSVTGKAEPA---RLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENN 230
                                    61        71        81        91       101       111       121        |-  |    141       151       161       171       181       191       201       211       221         
                                                                                                        130 134

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f (364)

Superfamily: p53-like transcription factors (153)

Family: T-box (4)

Protein domain: automated matches (2)

Human (Homo sapiens) [TaxId: 9606] (2)

d2x6ua_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.820, no name defined] (4)

Human (Homo sapiens) (3)

2x6uA00

A:52-230

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P53-like (54)

Family: T-box (3)

Homo sapiens (Human) (2)

T-box-2x6uA01

A:55-230

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Asymmetric/Biological 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
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PE4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Phe A:84 - Pro A:85	[ RasMol ]
		Ser A:141 - Pro A:142	[ RasMol ]

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

Access by PDB/NDB ID
	2x6u
		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
	TBX5_HUMAN \| Q99593
		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)
	142900
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

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
	TBX5_HUMAN \| Q99593
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TBX5_HUMAN \| Q99593	:	2x6v 4s0h 5bqd

2x6v	CRYSTAL STRUCTURE OF HUMAN TBX5 IN THE DNA -BOUND AND DNA-FREE FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 5)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (45, 45)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File