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- PDB-8cdn: Crystal structure of human Brachyury in complex with a single T b... -

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Basic information

Entry
Database: PDB / ID: 8cdn
TitleCrystal structure of human Brachyury in complex with a single T box binding element DNA
Components
  • DNA (5'-D(*AP*GP*GP*CP*TP*CP*AP*CP*AP*CP*CP*T)-3')
  • DNA (5'-D(*AP*GP*GP*TP*GP*TP*GP*AP*GP*CP*CP*T)-3')
  • T-box transcription factor T
KeywordsTRANSCRIPTION / Brachyury / TBXT
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 / regulation of transcription by RNA polymerase II / chromatin / 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, Brachyury / 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
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: 2.55 Å
AuthorsNewman, J.A. / Gavard, A.E. / von Delft, F. / Gileadi, O. / Bountra, C.
Funding support United States, 1items
OrganizationGrant numberCountry
The Mark Foundation United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into human brachyury DNA recognition and discovery of progressible binders for cancer therapy.
Authors: Newman, J.A. / Gavard, A.E. / Imprachim, N. / Aitkenhead, H. / Sheppard, H.E. / Te Poele, R. / Clarke, P.A. / Hossain, M.A. / Temme, L. / Oh, H.J. / Wells, C.I. / Davis-Gilbert, Z.W. / ...Authors: Newman, J.A. / Gavard, A.E. / Imprachim, N. / Aitkenhead, H. / Sheppard, H.E. / Te Poele, R. / Clarke, P.A. / Hossain, M.A. / Temme, L. / Oh, H.J. / Wells, C.I. / Davis-Gilbert, Z.W. / Workman, P. / Gileadi, O. / Drewry, D.H.
History
DepositionJan 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Feb 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-box transcription factor T
C: DNA (5'-D(*AP*GP*GP*TP*GP*TP*GP*AP*GP*CP*CP*T)-3')
D: DNA (5'-D(*AP*GP*GP*CP*TP*CP*AP*CP*AP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)29,3483
Polymers29,3483
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-26 kcal/mol
Surface area12560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.018, 63.018, 218.579
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein T-box transcription factor T / Brachyury protein / Protein T


Mass: 22022.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBXT, T / Production host: Escherichia coli (E. coli) / References: UniProt: O15178
#2: DNA chain DNA (5'-D(*AP*GP*GP*TP*GP*TP*GP*AP*GP*CP*CP*T)-3')


Mass: 3718.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*GP*GP*CP*TP*CP*AP*CP*AP*CP*CP*T)-3')


Mass: 3607.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


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

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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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: 0.1M ammonium acetate -- 0.1M bis-tris pH 5.5 -- 16%(w/v) PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.55→109 Å / Num. obs: 9158 / % possible obs: 100 % / Redundancy: 17.4 % / Biso Wilson estimate: 72.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.111 / Net I/σ(I): 15.9
Reflection shellResolution: 2.55→2.62 Å / Rmerge(I) obs: 2.863 / Mean I/σ(I) obs: 1 / Num. unique obs: 666 / CC1/2: 0.593

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→54.57 Å / SU ML: 0.326 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 35.7359
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3018 736 4.66 %
Rwork0.2733 15060 -
obs0.2747 9158 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.47 Å2
Refinement stepCycle: LAST / Resolution: 2.55→54.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1449 486 0 2 1937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612035
X-RAY DIFFRACTIONf_angle_d1.05532858
X-RAY DIFFRACTIONf_chiral_restr0.066308
X-RAY DIFFRACTIONf_plane_restr0.0086285
X-RAY DIFFRACTIONf_dihedral_angle_d29.8209784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.750.38271420.38493029X-RAY DIFFRACTION99.72
2.75-3.020.41011620.38362982X-RAY DIFFRACTION99.59
3.02-3.460.40481380.32893004X-RAY DIFFRACTION99.62
3.46-4.360.33471400.27573037X-RAY DIFFRACTION100
4.36-54.570.22881540.22343008X-RAY DIFFRACTION99.94

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