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- PDB-6f58: Crystal structure of human Brachyury (T) in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 6f58
TitleCrystal structure of human Brachyury (T) in complex with DNA
Components
  • Brachyury proteinT-box transcription factor T
  • DNA (5'-D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*TP*T)-3')
KeywordsTRANSCRIPTION / chordoma / Brachyury / T-box
Function / homology
Function and homology information


primitive streak formation / anterior/posterior axis specification, embryo / Epithelial-Mesenchymal Transition (EMT) during gastrulation / cardiac muscle cell myoblast differentiation / Germ layer formation at gastrulation / Formation of definitive endoderm / Formation of axial mesoderm / Cardiogenesis / cell fate specification / Formation of paraxial mesoderm ...primitive streak formation / anterior/posterior axis specification, embryo / Epithelial-Mesenchymal Transition (EMT) during gastrulation / cardiac muscle cell myoblast differentiation / Germ layer formation at gastrulation / Formation of definitive endoderm / Formation of axial mesoderm / Cardiogenesis / cell fate specification / Formation of paraxial mesoderm / mesoderm development / mesoderm formation / somitogenesis / heart morphogenesis / negative regulation of DNA-binding transcription factor activity / sequence-specific double-stranded DNA binding / RNA polymerase II-specific DNA-binding transcription factor 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 / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Transcription factor, T-box / Transcription factor, Brachyury / 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 ...Transcription factor, T-box / Transcription factor, Brachyury / 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 T
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.253 Å
AuthorsNewman, J.A. / Gavard, A.E. / Krojer, T. / Shrestha, L. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of human Brachyury (T) in complex with DNA
Authors: Newman, J.A. / Gavard, A.E. / Krojer, T. / Shrestha, L. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
History
DepositionDec 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*TP*T)-3')
D: DNA (5'-D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*TP*T)-3')
A: Brachyury protein
B: Brachyury protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8035
Polymers58,7804
Non-polymers231
Water6,035335
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, monomeric in abscence of DNA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-67 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.978, 37.109, 110.796
Angle α, β, γ (deg.)90.00, 103.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*TP*T)-3')


Mass: 7367.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein Brachyury protein / T-box transcription factor T / Protein T


Mass: 22022.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O15178
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 40% PEG300 -- 0.1M citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.25→29.65 Å / Num. obs: 27866 / % possible obs: 97.6 % / Redundancy: 3.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.079 / Net I/σ(I): 6.1
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2466 / CC1/2: 0.653 / Rpim(I) all: 0.501 / Rrim(I) all: 0.94 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XBR

1xbr


Resolution: 2.253→29.649 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 31.08
RfactorNum. reflection% reflection
Rfree0.2877 2571 5.01 %
Rwork0.2423 --
obs0.2445 51343 93.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.253→29.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2843 952 1 335 4131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043988
X-RAY DIFFRACTIONf_angle_d0.6825598
X-RAY DIFFRACTIONf_dihedral_angle_d17.1952197
X-RAY DIFFRACTIONf_chiral_restr0.044607
X-RAY DIFFRACTIONf_plane_restr0.005552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2526-2.29590.40081500.34242492X-RAY DIFFRACTION87
2.2959-2.34270.34341480.32642778X-RAY DIFFRACTION95
2.3427-2.39360.34951380.31782728X-RAY DIFFRACTION95
2.3936-2.44930.3771370.32152767X-RAY DIFFRACTION95
2.4493-2.51050.4061320.31452730X-RAY DIFFRACTION94
2.5105-2.57830.34971480.30232664X-RAY DIFFRACTION93
2.5783-2.65420.47751390.30242786X-RAY DIFFRACTION96
2.6542-2.73980.31511570.28692703X-RAY DIFFRACTION96
2.7398-2.83760.31291760.27372805X-RAY DIFFRACTION96
2.8376-2.95110.34321310.27722762X-RAY DIFFRACTION97
2.9511-3.08530.2871770.26132845X-RAY DIFFRACTION96
3.0853-3.24780.29411420.23052689X-RAY DIFFRACTION94
3.2478-3.4510.26681390.21112682X-RAY DIFFRACTION92
3.451-3.7170.24091080.21982651X-RAY DIFFRACTION91
3.717-4.09020.23411460.20132658X-RAY DIFFRACTION92
4.0902-4.680.20561370.18692719X-RAY DIFFRACTION94
4.68-5.88880.27331300.212664X-RAY DIFFRACTION93
5.8888-29.65170.24731360.22582649X-RAY DIFFRACTION91

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