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- PDB-4s0h: TBX5 DB, NKX2.5 HD, ANF DNA Complex -

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Basic information

Entry
Database: PDB / ID: 4s0h
TitleTBX5 DB, NKX2.5 HD, ANF DNA Complex
Components
  • 5'-D(*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP*A)-3'
  • 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP*TP*GP*AP*AP*GP*TP*GP*G)-3'
  • Homeobox protein Nkx-2.5
  • T-box transcription factor TBX5
KeywordsTRANSCRIPTION/DNA / Transcription Factor / TRANSCRIPTION-DNA complex
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 / Nkx-2.5 complex / atrioventricular bundle cell differentiation / Purkinje myocyte differentiation / right ventricular cardiac muscle tissue morphogenesis / septum secundum development / proepicardium development / pulmonary myocardium development ...cardiac left ventricle formation / positive regulation of cell communication by electrical coupling involved in cardiac conduction / positive regulation of cardiac conduction / Nkx-2.5 complex / atrioventricular bundle cell differentiation / Purkinje myocyte differentiation / right ventricular cardiac muscle tissue morphogenesis / septum secundum development / proepicardium development / pulmonary myocardium development / 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 / cardiac ventricle formation / apoptotic process involved in heart morphogenesis / atrioventricular node cell fate commitment / cell migration involved in coronary vasculogenesis / bundle of His development / atrial cardiac muscle cell development / ventricular cardiac myofibril assembly / sinoatrial node development / atrioventricular node cell development / embryonic heart tube left/right pattern formation / positive regulation of cardioblast differentiation / forelimb morphogenesis / atrial cardiac muscle tissue development / atrioventricular node development / ventricular cardiac muscle cell development / regulation of cardiac muscle cell proliferation / atrial septum morphogenesis / endocardial cushion development / positive regulation of heart contraction / Physiological factors / pericardium development / negative regulation of myotube differentiation / negative regulation of cardiac muscle cell proliferation / cardiac conduction system development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / regulation of atrial cardiac muscle cell membrane depolarization / pattern specification process / negative regulation of epithelial to mesenchymal transition / pharyngeal system development / positive regulation of sodium ion transport / negative regulation of epithelial cell apoptotic process / outflow tract septum morphogenesis / cardiac muscle tissue morphogenesis / ventricular trabecula myocardium morphogenesis / heart trabecula formation / adult heart development / embryonic heart tube development / embryonic forelimb morphogenesis / aortic valve morphogenesis / cardiac muscle cell development / embryonic limb morphogenesis / Cardiogenesis / cell fate specification / negative regulation of cardiac muscle cell apoptotic process / atrioventricular valve morphogenesis / cardiac muscle cell proliferation / epithelial cell apoptotic process / ventricular septum development / DNA-binding transcription activator activity / ventricular septum morphogenesis / heart looping / cardiac septum morphogenesis / positive regulation of gap junction assembly / thyroid gland development / hemopoiesis / regulation of cardiac conduction / positive regulation of transcription initiation by RNA polymerase II / regulation of cardiac muscle contraction / vasculogenesis / heart morphogenesis / positive regulation of cardiac muscle cell proliferation / cardiac muscle contraction / spleen development / epithelial cell differentiation / positive regulation of neuron differentiation / negative regulation of cell migration / epithelial cell proliferation / positive regulation of epithelial cell proliferation / protein-DNA complex / morphogenesis of an epithelium / lung development / negative regulation of canonical Wnt signaling pathway / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / 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 / cell differentiation / transcription cis-regulatory region binding / 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
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 / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / p53-like transcription factor, DNA-binding / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Homeobox protein Nkx-2.5 / T-box transcription factor TBX5
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.817 Å
AuthorsPradhan, L.
CitationJournal: Biochemistry / Year: 2016
Title: Intermolecular Interactions of Cardiac Transcription Factors NKX2.5 and TBX5.
Authors: Pradhan, L. / Gopal, S. / Li, S. / Ashur, S. / Suryanarayanan, S. / Kasahara, H. / Nam, H.J.
History
DepositionDec 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Homeobox protein Nkx-2.5
E: T-box transcription factor TBX5
F: Homeobox protein Nkx-2.5
C: 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP*TP*GP*AP*AP*GP*TP*GP*G)-3'
D: 5'-D(*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP*A)-3'
G: 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP*TP*GP*AP*AP*GP*TP*GP*G)-3'
H: 5'-D(*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP*A)-3'


Theoretical massNumber of molelcules
Total (without water)79,1568
Polymers79,1568
Non-polymers00
Water362
1
A: T-box transcription factor TBX5
B: Homeobox protein Nkx-2.5
C: 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP*TP*GP*AP*AP*GP*TP*GP*G)-3'
D: 5'-D(*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP*A)-3'


Theoretical massNumber of molelcules
Total (without water)39,5784
Polymers39,5784
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: T-box transcription factor TBX5
F: Homeobox protein Nkx-2.5
G: 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP*TP*GP*AP*AP*GP*TP*GP*G)-3'
H: 5'-D(*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP*A)-3'


Theoretical massNumber of molelcules
Total (without water)39,5784
Polymers39,5784
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.217, 78.459, 78.695
Angle α, β, γ (deg.)90.00, 108.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein T-box transcription factor TBX5 / T-box protein 5


Mass: 21396.799 Da / Num. of mol.: 2 / Fragment: DB (UNP residues 53-238)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBX5 / Production host: unidentified (others) / References: UniProt: Q99593
#2: Protein Homeobox protein Nkx-2.5 / / Cardiac-specific homeobox / Homeobox protein CSX / Homeobox protein NK-2 homolog E


Mass: 6531.528 Da / Num. of mol.: 2 / Fragment: HD (UNP residues 142-194)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NKX2-5, CSX, NKX2.5, NKX2E / Production host: unidentified (others) / References: UniProt: P52952
#3: DNA chain 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP*TP*GP*AP*AP*GP*TP*GP*G)-3'


Mass: 5795.760 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: ANF DNA strand 1 / Source: (synth.) synthetic construct (others)
#4: DNA chain 5'-D(*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP*A)-3'


Mass: 5853.812 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: ANF DNA strand 2 / Source: (synth.) synthetic construct (others)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.55 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9767 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9767 Å / Relative weight: 1
ReflectionResolution: 2.817→74.481 Å / Num. all: 19742 / Num. obs: 18168 / % possible obs: 99.9 % / Redundancy: 3.6 %
Reflection shellHighest resolution: 2.817 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.817→38.164 Å / SU ML: 0.38 / σ(F): 0.12 / Phase error: 28.93 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2475 1807 10 %
Rwork0.1888 --
obs0.1946 18072 91.58 %
all-18168 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.3562 Å20 Å2-8.6444 Å2
2--27.0418 Å2-0 Å2
3----17.6856 Å2
Refinement stepCycle: LAST / Resolution: 2.817→38.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 1546 0 2 5350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115636
X-RAY DIFFRACTIONf_angle_d1.3877931
X-RAY DIFFRACTIONf_dihedral_angle_d25.2652213
X-RAY DIFFRACTIONf_chiral_restr0.063861
X-RAY DIFFRACTIONf_plane_restr0.008740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8166-2.89270.4249920.316835X-RAY DIFFRACTION61
2.8927-2.97780.41571150.29211035X-RAY DIFFRACTION77
2.9778-3.07390.35491190.28891080X-RAY DIFFRACTION80
3.0739-3.18370.36691390.251247X-RAY DIFFRACTION91
3.1837-3.31110.32411440.20951288X-RAY DIFFRACTION96
3.3111-3.46170.23691490.19371331X-RAY DIFFRACTION98
3.4617-3.6440.25141490.2071342X-RAY DIFFRACTION98
3.644-3.87220.24291490.18911346X-RAY DIFFRACTION99
3.8722-4.17080.24661490.18171335X-RAY DIFFRACTION97
4.1708-4.58990.22651490.16281344X-RAY DIFFRACTION98
4.5899-5.25260.23011500.1551351X-RAY DIFFRACTION99
5.2526-6.61210.21431520.17021374X-RAY DIFFRACTION99
6.6121-38.16750.1841510.16231357X-RAY DIFFRACTION96

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