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- PDB-4a04: Structure of the DNA-bound T-box domain of human TBX1, a transcri... -

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Basic information

Entry
Database: PDB / ID: 4a04
TitleStructure of the DNA-bound T-box domain of human TBX1, a transcription factor associated with the DiGeorge syndrome
Components
  • DNA
  • T-BOX TRANSCRIPTION FACTOR TBX1
KeywordsTRANSCRIPTION / T-BOX PROTEINS / PROTEIN-DNA INTERACTION
Function / homology
Function and homology information


regulation of animal organ morphogenesis / positive regulation of tongue muscle cell differentiation / muscle cell fate commitment / semicircular canal morphogenesis / vagus nerve morphogenesis / soft palate development / tongue morphogenesis / ear morphogenesis / muscle tissue morphogenesis / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 ...regulation of animal organ morphogenesis / positive regulation of tongue muscle cell differentiation / muscle cell fate commitment / semicircular canal morphogenesis / vagus nerve morphogenesis / soft palate development / tongue morphogenesis / ear morphogenesis / muscle tissue morphogenesis / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / muscle organ morphogenesis / embryonic viscerocranium morphogenesis / parathyroid gland development / cochlea morphogenesis / aorta morphogenesis / negative regulation of mesenchymal cell apoptotic process / mesenchymal cell apoptotic process / enamel mineralization / chromatin => GO:0000785 / lymph vessel development / pattern specification process / pharyngeal system development / coronary artery morphogenesis / outflow tract septum morphogenesis / embryonic cranial skeleton morphogenesis / cellular response to fibroblast growth factor stimulus / outer ear morphogenesis / middle ear morphogenesis / determination of left/right symmetry / cell fate specification / blood vessel morphogenesis / face morphogenesis / neural crest cell migration / muscle organ development / anterior/posterior pattern specification / positive regulation of mesenchymal cell proliferation / artery morphogenesis / inner ear morphogenesis / blood vessel development / outflow tract morphogenesis / odontogenesis of dentin-containing tooth / social behavior / mesoderm development / negative regulation of cell differentiation / thyroid gland development / retinoic acid receptor signaling pathway / heart morphogenesis / cellular response to retinoic acid / epithelial cell differentiation / thymus development / positive regulation of epithelial cell proliferation / sensory perception of sound / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / cell population proliferation / sequence-specific DNA binding / positive regulation of MAPK cascade / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Transcription factor, T-box / 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 ...Transcription factor, T-box / 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 TBX1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsEl Omari, K. / De Mesmaeker, J. / Karia, D. / Ginn, H. / Bhattacharya, S. / Mancini, E.J.
CitationJournal: Proteins / Year: 2012
Title: Structure of the DNA-Bound T-Box Domain of Human Tbx1, a Transcription Factor Associated with the Digeorge Syndrome
Authors: El Omari, K. / De Mesmaeker, J. / Karia, D. / Ginn, H. / Bhattacharya, S. / Mancini, E.J.
History
DepositionSep 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Structure summary
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Apr 18, 2012Group: Other
Revision 1.4Sep 12, 2012Group: Refinement description
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-BOX TRANSCRIPTION FACTOR TBX1
B: T-BOX TRANSCRIPTION FACTOR TBX1
D: DNA
E: DNA


Theoretical massNumber of molelcules
Total (without water)62,4044
Polymers62,4044
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-47.1 kcal/mol
Surface area26680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.420, 92.740, 101.020
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 TBX1 / TBX1 / T-BOX PROTEIN 1 / TESTIS-SPECIFIC T-BOX PROTEIN


Mass: 23834.170 Da / Num. of mol.: 2 / Fragment: TBOX DOMAIN, RESIDUES 109-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O43435
#2: DNA chain DNA /


Mass: 7367.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.68 Å3/Da / Density % sol: 54.11 % / Description: NONE
Crystal growpH: 5
Details: 5% (W/V) POLYETHYLENE GLYCOL 6000, 100 MM CITRATE PH 5

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.58→71.4 Å / Num. obs: 21470 / % possible obs: 98.8 % / Observed criterion σ(I): 2.3 / Redundancy: 6.4 % / Biso Wilson estimate: 79.43 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.9
Reflection shellResolution: 2.58→2.64 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XBR

1xbr


Resolution: 2.58→68.32 Å / Cor.coef. Fo:Fc: 0.9288 / Cor.coef. Fo:Fc free: 0.9222 / SU R Cruickshank DPI: 0.468 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.496 / SU Rfree Blow DPI: 0.255 / SU Rfree Cruickshank DPI: 0.254 / Details: RESIDUES 250-257 DISORDERED IN CHAIN A
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1100 5.12 %RANDOM
Rwork0.2065 ---
obs0.2076 21470 98.83 %-
Displacement parametersBiso mean: 69.48 Å2
Baniso -1Baniso -2Baniso -3
1-12.395 Å20 Å20 Å2
2---16.8065 Å20 Å2
3---4.4115 Å2
Refine analyzeLuzzati coordinate error obs: 0.444 Å
Refinement stepCycle: LAST / Resolution: 2.58→68.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 957 0 66 4062
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0074198HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.065875HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1634SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes500HARMONIC5
X-RAY DIFFRACTIONt_it4198HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.18
X-RAY DIFFRACTIONt_other_torsion19.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion525SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4055SEMIHARMONIC4
LS refinement shellResolution: 2.58→2.71 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3036 135 4.81 %
Rwork0.2533 2674 -
all0.2558 2809 -
obs--98.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5445-0.710.38171.3381-0.6223.7838-0.0009-0.10840.25750.01560.017-0.1326-0.02430.1905-0.0161-0.16360.00520.04290.00780.0037-0.0195-23.831441.0857-6.2341
22.6765-0.0460.19761.06990.30264.5990.0045-0.2464-0.1797-0.0630.0675-0.07980.1001-0.2905-0.0721-0.1530.0077-0.0466-0.0093-0.0161-0.0543-11.70484.1416-10.4055
31.4678-1.7212-0.66892.52080.65430.6701-0.0360.14260.0294-0.10340.0056-0.0467-0.0324-0.00680.0304-0.09210.1843-0.00550.1172-0.0219-0.0322-18.326725.6331-27.9328
41.8731-1.6124-0.42462.63590.78450.6296-0.02550.1028-0.0244-0.06830.0031-0.01170.0095-0.17520.0223-0.18020.20340.09360.12780.0605-0.0193-18.353724.4595-27.6744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN D
4X-RAY DIFFRACTION4CHAIN E

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