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- PDB-2x6u: Crystal structure of human TBX5 in the DNA-free form -

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Basic information

Entry
Database: PDB / ID: 2x6u
TitleCrystal structure of human TBX5 in the DNA-free form
ComponentsT-BOX TRANSCRIPTION FACTOR TBX5
KeywordsTRANSCRIPTION / DEVELOPMENTAL PROTEIN / DNA-BINDING / HOLT-ORAM-SYNDROME / IG-FOLD / NUCLEAR PROTEIN / REPRESSOR / TBX3 / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


cardiac left ventricle formation / positive regulation of cell communication by electrical coupling involved in cardiac conduction / positive regulation of cardiac conduction / atrioventricular bundle cell differentiation / positive regulation of secondary heart field cardioblast proliferation / cell-cell signaling involved in cardiac conduction / bundle of His cell to Purkinje myocyte communication by electrical coupling / atrioventricular node cell fate commitment / cell migration involved in coronary vasculogenesis / bundle of His development ...cardiac left ventricle formation / positive regulation of cell communication by electrical coupling involved in cardiac conduction / positive regulation of cardiac conduction / atrioventricular bundle cell differentiation / positive regulation of secondary heart field cardioblast proliferation / cell-cell signaling involved in cardiac conduction / bundle of His cell to Purkinje myocyte communication by electrical coupling / atrioventricular node cell fate commitment / cell migration involved in coronary vasculogenesis / bundle of His development / sinoatrial node development / atrioventricular node cell development / positive regulation of cardioblast differentiation / forelimb morphogenesis / atrial septum morphogenesis / endocardial cushion development / Physiological factors / pericardium development / negative regulation of cardiac muscle cell proliferation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / regulation of atrial cardiac muscle cell membrane depolarization / negative regulation of epithelial to mesenchymal transition / pattern specification process / embryonic forelimb morphogenesis / embryonic limb morphogenesis / Cardiogenesis / cell fate specification / atrioventricular valve morphogenesis / cardiac muscle cell proliferation / ventricular septum development / positive regulation of gap junction assembly / positive regulation of cardiac muscle cell proliferation / negative regulation of cell migration / protein-DNA complex / morphogenesis of an epithelium / lung development / cell-cell signaling / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription factor, T-box / T-box transcription factor, DNA-binding domain / T-box transcription factor / Transcription factor, T-box, conserved site / T-box superfamily / T-box domain signature 2. / T-box domain signature 1. / T-box domain profile. / Domain first found in the mice T locus (Brachyury) protein / T-box ...Transcription factor, T-box / T-box transcription factor, DNA-binding domain / T-box transcription factor / Transcription factor, T-box, conserved site / T-box superfamily / T-box domain signature 2. / T-box domain signature 1. / T-box domain profile. / Domain first found in the mice T locus (Brachyury) protein / T-box / p53-like transcription factor, DNA-binding / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-box transcription factor TBX5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStirnimann, C.U. / Mueller, C.W.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural Basis of Tbx5-DNA Recognition: The T-Box Domain in its DNA-Bound and -Unbound Form.
Authors: Stirnimann, C.U. / Ptchelkine, D. / Grimm, C. / Muller, C.W.
History
DepositionFeb 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-BOX TRANSCRIPTION FACTOR TBX5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8586
Polymers23,4061
Non-polymers4525
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.710, 69.850, 80.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein T-BOX TRANSCRIPTION FACTOR TBX5 / HUMAN TBX5 / T-BOX PROTEIN 5 / TBX5


Mass: 23406.096 Da / Num. of mol.: 1 / Fragment: T-BOX DOMAIN, RESIDUES 51-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-M11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) RIPL / References: UniProt: Q99593
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.21 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 16939 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 25.05 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.1
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WWPDB DEPOSITION 43002

Resolution: 1.9→19.662 Å / SU ML: 0.24 / σ(F): 1.99 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 847 5 %
Rwork0.2105 --
obs0.2131 16922 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.11 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.041 Å2-0 Å2-0 Å2
2---4.8972 Å2-0 Å2
3----9.5941 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 20 150 1603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031545
X-RAY DIFFRACTIONf_angle_d0.7082095
X-RAY DIFFRACTIONf_dihedral_angle_d14.52586
X-RAY DIFFRACTIONf_chiral_restr0.049228
X-RAY DIFFRACTIONf_plane_restr0.003263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.01890.28771400.24882650X-RAY DIFFRACTION100
2.0189-2.17460.27941380.22272623X-RAY DIFFRACTION100
2.1746-2.39310.29161390.21192645X-RAY DIFFRACTION100
2.3931-2.73860.2831400.22882647X-RAY DIFFRACTION100
2.7386-3.44740.25671410.20522696X-RAY DIFFRACTION100
3.4474-19.66310.22651490.18952814X-RAY DIFFRACTION100

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