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- PDB-6f59: Crystal structure of human Brachyury (T) G177D variant in complex... -

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Basic information

Entry
Database: PDB / ID: 6f59
TitleCrystal structure of human Brachyury (T) G177D variant in complex with DNA
Components
  • Brachyury protein
  • DNA (26-MER)
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 / 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, T-box / 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 ...Transcription factor, T-box / 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 / 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: 2.151 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: 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
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
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

Downloads & links

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Assembly

Deposited unit
C: DNA (26-MER)
D: DNA (26-MER)
A: Brachyury protein
B: Brachyury protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2746
Polymers60,1334
Non-polymers1412
Water2,018112
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-71 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.270, 75.270, 288.468
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21B-344-

HOH

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Components

#1: DNA chain DNA (26-MER)


Mass: 7986.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein Brachyury protein / Protein T


Mass: 22080.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Variant: G177D / 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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.4 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 56% MPD -- 0.1M SPG pH 6.0

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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: 2.15→144.23 Å / Num. obs: 46387 / % possible obs: 99.9 % / Redundancy: 25.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.024 / Rrim(I) all: 0.117 / Net I/σ(I): 12.9
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 23.1 % / Rmerge(I) obs: 2.618 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3687 / CC1/2: 0.777 / Rpim(I) all: 0.55 / Rrim(I) all: 2.677 / % possible all: 98.7

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Processing

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

1xbr


Resolution: 2.151→72.831 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.59
RfactorNum. reflection% reflection
Rfree0.252 2303 5.03 %
Rwork0.2214 --
obs0.2229 45750 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.151→72.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 1060 9 112 4105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084207
X-RAY DIFFRACTIONf_angle_d0.9635911
X-RAY DIFFRACTIONf_dihedral_angle_d16.4922311
X-RAY DIFFRACTIONf_chiral_restr0.054640
X-RAY DIFFRACTIONf_plane_restr0.006576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1509-2.19770.39271390.35112532X-RAY DIFFRACTION95
2.1977-2.24880.3971360.33562591X-RAY DIFFRACTION97
2.2488-2.3050.37921440.30982625X-RAY DIFFRACTION97
2.305-2.36740.30291240.28762663X-RAY DIFFRACTION98
2.3674-2.4370.30851540.28382635X-RAY DIFFRACTION98
2.437-2.51570.31171490.2832651X-RAY DIFFRACTION98
2.5157-2.60560.33591310.28722693X-RAY DIFFRACTION99
2.6056-2.70990.33481340.28172697X-RAY DIFFRACTION99
2.7099-2.83330.2911380.28822708X-RAY DIFFRACTION99
2.8333-2.98270.31041360.28512740X-RAY DIFFRACTION100
2.9827-3.16950.32991500.27062727X-RAY DIFFRACTION100
3.1695-3.41430.28041440.23892761X-RAY DIFFRACTION100
3.4143-3.75780.25291500.22992760X-RAY DIFFRACTION100
3.7578-4.30150.21971500.18762785X-RAY DIFFRACTION100
4.3015-5.41920.19591700.18072845X-RAY DIFFRACTION100
5.4192-72.87290.21931540.1893034X-RAY DIFFRACTION100

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