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- PDB-1h6f: Human TBX3, a transcription factor responsible for ulnar-mammary ... -

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Basic information

Entry
Database: PDB / ID: 1h6f
TitleHuman TBX3, a transcription factor responsible for ulnar-mammary syndrome, bound to a palindromic DNA site
Components
  • 5'-D(*TP*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP* AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*T)-3'
  • T-BOX TRANSCRIPTION FACTOR TBX3
KeywordsTRANSCRIPTION FACTOR / TBX3 / T-BOX TRANSCRIPTION FACTOR / ULNAR-MAMMARY SYNDROME / HOLT-ORAM-SYNDROME / IG-FOLD / DNA-BINDING / REPRESSOR / NUCLEAR PROTEIN / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


mesoderm morphogenesis / mammary placode formation / ureteric peristalsis / negative regulation of cell proliferation involved in heart morphogenesis / sinoatrial node cell development / hepatoblast differentiation / atrioventricular bundle cell differentiation / specification of animal organ position / semicircular canal morphogenesis / female genitalia development ...mesoderm morphogenesis / mammary placode formation / ureteric peristalsis / negative regulation of cell proliferation involved in heart morphogenesis / sinoatrial node cell development / hepatoblast differentiation / atrioventricular bundle cell differentiation / specification of animal organ position / semicircular canal morphogenesis / female genitalia development / cardiac jelly development / limbic system development / luteinizing hormone secretion / follicle-stimulating hormone secretion / atrioventricular canal morphogenesis / forelimb morphogenesis / anterior/posterior axis specification, embryo / cardiac muscle cell fate commitment / atrioventricular canal development / cardiac epithelial to mesenchymal transition / smooth muscle cell differentiation / regulation of protein complex stability / endocardial cushion formation / male genitalia development / negative regulation of myoblast differentiation / negative regulation of stem cell differentiation / mammary gland development / branching involved in mammary gland duct morphogenesis / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / cell fate specification / embryonic digit morphogenesis / stem cell population maintenance / ventricular septum morphogenesis / negative regulation of epithelial cell differentiation / blood vessel development / positive regulation of stem cell proliferation / heart looping / roof of mouth development / outflow tract morphogenesis / positive regulation of cell cycle / Transcriptional and post-translational regulation of MITF-M expression and activity / animal organ morphogenesis / stem cell proliferation / skeletal system development / regulation of protein stability / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / cellular senescence / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cilium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
T-box transcription factor 2/3, transcription activation domain / : / T-box transcription factor 2/3, TAD domain / T-box transcription factor 2/3, repressor domain / Transcription factor, T-box / T-box transcription factor / Transcription factor, T-box, conserved site / T-box superfamily / T-box transcription factor, DNA-binding domain / T-box domain signature 2. ...T-box transcription factor 2/3, transcription activation domain / : / T-box transcription factor 2/3, TAD domain / T-box transcription factor 2/3, repressor domain / Transcription factor, T-box / T-box transcription factor / Transcription factor, T-box, conserved site / T-box superfamily / T-box transcription factor, DNA-binding domain / 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 TBX3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsColl, M. / Muller, C.W.
Citation
Journal: Structure / Year: 2002
Title: Structure of the DNA-Bound T-Box Domain of Human Tbx3, a Transcription Factor Responsible for Ulnar- Mammary Syndrome
Authors: Coll, M. / Seidman, J.G. / Muller, C.W.
#1: Journal: Nature / Year: 1997
Title: Crystallographic Structure of the T Domain-DNA Complex of the Brachyury Transcription Factor
Authors: Muller, C.W. / Hermann, B.
History
DepositionJun 13, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Advisory / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / struct
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _struct.title
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-BOX TRANSCRIPTION FACTOR TBX3
B: T-BOX TRANSCRIPTION FACTOR TBX3
C: 5'-D(*TP*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP* AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*T)-3'
D: 5'-D(*TP*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP* AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1575
Polymers60,1324
Non-polymers241
Water11,007611
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.040, 104.910, 125.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99996, 0.00365, 0.00778), (0.00359, 0.99996, -0.00813), (-0.00781, -0.0081, -0.99994)
Vector: 14.478, 0.52063, 63.14726)

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Components

#1: Protein T-BOX TRANSCRIPTION FACTOR TBX3 / TBX3 TRANSCRIPTION FACTOR / T-BOX PROTEIN 3


Mass: 22698.367 Da / Num. of mol.: 2 / Fragment: T-DOMAIN RESIDUES 101-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PT7-7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15119
#2: DNA chain 5'-D(*TP*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP* AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*T)-3'


Mass: 7367.791 Da / Num. of mol.: 2 / Fragment: PALINDROMIC BINDING SITE / Source method: obtained synthetically / Source: (synth.) SYNTHETIC (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTRANSCRIPTIONAL REPRESSOR INVOLVED IN DEVELOPMENTAL PROCESSES.
Sequence detailsFIRST TWO RESIDUES, MET AND LYS, WERE ADDED AT THE N-TERMINUS FOR CLONING AND EXPRESSION THE ...FIRST TWO RESIDUES, MET AND LYS, WERE ADDED AT THE N-TERMINUS FOR CLONING AND EXPRESSION THE PROTEIN IS THE SPLICE ISOFORM I

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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: 2.1 Å3/Da / Density % sol: 42.35 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.76 mMDNA duplex1drop
20.59 mMprotein1drop
340 mMmagnesium acetate1reservoir
450 mMsodium cacodylate1reservoirpH6.0
530 %MPD1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.956
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 55690 / % possible obs: 96.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4 / % possible all: 91.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 204582 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 91.1 % / Rmerge(I) obs: 0.298

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XBR

1xbr


Resolution: 1.7→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 -9.7 %RANDOM
Rwork0.2007 ---
obs0.2007 55690 96.6 %-
Displacement parametersBiso mean: 25.0945 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3065 978 1 611 4655
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.8581.5
X-RAY DIFFRACTIONc_mcangle_it2.0262
X-RAY DIFFRACTIONc_scbond_it1.9362
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.2974 491
Rwork-4626
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.2007 / Rfactor Rfree: 0.2388 / Rfactor Rwork: 0.2007
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.2974

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