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- PDB-7zkf: Crystal Structure of human Brachyury G177D variant in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7zkf
TitleCrystal Structure of human Brachyury G177D variant in complex with CF-5-86
ComponentsT-box transcription factor T
KeywordsTRANSCRIPTION / Brachyury / Chordoma
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 / cell fate specification / Cardiogenesis / 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 / cell fate specification / Cardiogenesis / Formation of paraxial mesoderm / mesoderm development / mesoderm formation / somitogenesis / heart morphogenesis / sequence-specific double-stranded DNA binding / transcription corepressor activity / 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
: / PHOSPHATE ION / T-box transcription factor T
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.49 Å
AuthorsNewman, J.A. / Gavard, A. / Aitkenhead, H. / Imprachim, N. / Sherestha, L. / Burgess-Brown, N.A. / von Delft, F. / Bountra, C. / Gileadi, O.
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
DepositionApr 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.0Feb 19, 2025Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_database_status / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id
Revision 2.1Feb 26, 2025Group: Database references / Category: citation / citation_author
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
A: T-box transcription factor T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0103
Polymers19,6561
Non-polymers3542
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-0 kcal/mol
Surface area9490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.960, 99.960, 99.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-302-

PO4

21A-302-

PO4

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Components

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


Mass: 19655.623 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: Chemical ChemComp-A1I1T / N-(4-((2-fluorophenyl)(hydroxy)methyl)phenyl)acetamide / ~{N}-[4-[(~{R})-(2-fluorophenyl)-oxidanyl-methyl]phenyl]ethanamide


Mass: 259.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14FNO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M SPG pH 7.0, 30 % PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.49→42.98 Å / Num. obs: 24512 / % possible obs: 79.02 % / Redundancy: 16 % / CC1/2: 0.99 / Rmerge(I) obs: 0.045 / Net I/σ(I): 32.76
Reflection shellResolution: 1.493→1.546 Å / Rmerge(I) obs: 0.7466 / Mean I/σ(I) obs: 0.81 / Num. unique obs: 718 / CC1/2: 0.617 / % possible all: 23.11

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.49→42.98 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 1210 4.94 %
Rwork0.1814 --
obs0.1833 24508 79.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 24 234 1638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061529
X-RAY DIFFRACTIONf_angle_d0.8322083
X-RAY DIFFRACTIONf_dihedral_angle_d27.354587
X-RAY DIFFRACTIONf_chiral_restr0.086215
X-RAY DIFFRACTIONf_plane_restr0.005273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.550.3698350.3486790X-RAY DIFFRACTION24
1.55-1.620.2674750.25871535X-RAY DIFFRACTION47
1.62-1.710.24731020.2312000X-RAY DIFFRACTION62
1.71-1.820.26491490.22262574X-RAY DIFFRACTION80
1.82-1.960.26231700.21083191X-RAY DIFFRACTION98
1.96-2.150.22041600.20233242X-RAY DIFFRACTION100
2.15-2.460.2631600.19463296X-RAY DIFFRACTION100
2.46-3.110.22861680.19083291X-RAY DIFFRACTION100
3.11-42.980.18871910.15453379X-RAY DIFFRACTION100

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