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- PDB-2x6v: Crystal structure of human TBX5 in the DNA-bound and DNA-free form -

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Basic information

Entry
Database: PDB / ID: 2x6v
TitleCrystal structure of human TBX5 in the DNA-bound and DNA-free form
Components
  • 5'-D(*TP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP)-3'
  • 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP)-3'
  • T-BOX TRANSCRIPTION FACTOR TBX5
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX / HOLT-ORAM-SYNDROME / DEVELOPMENTAL PROTEIN / TRANSCRIPTION REGULATION / REPRESSOR / DNA-BINDING / TRANSCRIPTION / NUCLEAR PROTEIN
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
DNA / DNA (> 10) / T-box transcription factor TBX5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPtchelkine, D. / Stirnimann, C.U. / Grimm, C. / 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
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
B: T-BOX TRANSCRIPTION FACTOR TBX5
C: 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP)-3'
D: 5'-D(*TP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9137
Polymers53,5104
Non-polymers4033
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-49.5 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.240, 118.240, 243.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 23406.096 Da / Num. of mol.: 2 / Fragment: T-BOX DOMAIN, RESIDUES 51-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROX HTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99593

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP)-3'


Mass: 3244.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*TP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP)-3'


Mass: 3453.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 371 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 4.66 Å3/Da / Density % sol: 73.39 % / Description: NONE
Crystal growpH: 5.6
Details: 0.1 M MES PH 5.6, 0.2 M MGCL2, 0.2 M NACL, 5% PEG 6K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 51044 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.8 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6F

1h6f


Resolution: 2.2→19.707 Å / σ(F): 1.36 / Phase error: 20.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 2553 5 %
Rwork0.1973 --
obs0.1986 51040 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.064 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 49.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.1497 Å20 Å20 Å2
2---2.1497 Å20 Å2
3---4.2994 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 428 26 368 3671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093534
X-RAY DIFFRACTIONf_angle_d1.2614870
X-RAY DIFFRACTIONf_dihedral_angle_d19.7911347
X-RAY DIFFRACTIONf_chiral_restr0.072523
X-RAY DIFFRACTIONf_plane_restr0.005543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.24230.29681300.26642466X-RAY DIFFRACTION94
2.2423-2.2880.3061410.25352678X-RAY DIFFRACTION100
2.288-2.33760.25881400.25662663X-RAY DIFFRACTION100
2.3376-2.39190.2781410.23212665X-RAY DIFFRACTION100
2.3919-2.45160.23611400.21132672X-RAY DIFFRACTION100
2.4516-2.51780.25111410.20162684X-RAY DIFFRACTION100
2.5178-2.59170.24561420.21042681X-RAY DIFFRACTION100
2.5917-2.67520.22191410.20262685X-RAY DIFFRACTION100
2.6752-2.77050.2621410.20992673X-RAY DIFFRACTION100
2.7705-2.88110.23011420.20332699X-RAY DIFFRACTION100
2.8811-3.01180.25191420.21752701X-RAY DIFFRACTION100
3.0118-3.170.28161420.20252696X-RAY DIFFRACTION100
3.17-3.36770.21671430.18372722X-RAY DIFFRACTION100
3.3677-3.62620.19561430.16982718X-RAY DIFFRACTION100
3.6262-3.98840.1761450.16452756X-RAY DIFFRACTION100
3.9884-4.55930.16251460.15282778X-RAY DIFFRACTION100
4.5593-5.72090.17531480.15292798X-RAY DIFFRACTION99
5.7209-19.70740.22341450.18622752X-RAY DIFFRACTION92

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