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- PDB-8a10: Crystal Structure of human Brachyury G177D variant in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8a10
TitleCrystal Structure of human Brachyury G177D variant in complex with Molpolrt-020-049-143
ComponentsT-box transcription factor T
KeywordsTRANSCRIPTION / Chordoma / Brachyury / Transcription factor
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
: / T-box transcription factor T
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.88 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
DepositionMay 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.0Jan 22, 2025Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact
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 / _pdbx_validate_close_contact.auth_seq_id_1
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)19,9992
Polymers19,6561
Non-polymers3441
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.395, 100.395, 99.437
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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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-A1IYK / 5-[[(3S)-1-(2-chlorophenyl)-2-oxidanylidene-pyrrolidin-3-yl]amino]-2-methyl-benzamide / 5-{[1-(2-chlorophenyl)-2-oxopyrrolidin-3-yl]amino}-2-methylbenzamide


Mass: 343.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18ClN3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / 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: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.88→50.198 Å / Num. obs: 14222 / % possible obs: 89.7 % / Redundancy: 19.8 % / Biso Wilson estimate: 31.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.052 / Net I/σ(I): 9.3
Reflection shellResolution: 1.88→1.91 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 568 / CC1/2: 0.309 / Rpim(I) all: 1.437

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.88→39.83 Å / SU ML: 0.2924 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.5913
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2723 725 5.16 %
Rwork0.2036 13338 -
obs0.2073 14063 88.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.09 Å2
Refinement stepCycle: LAST / Resolution: 1.88→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 24 225 1629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611462
X-RAY DIFFRACTIONf_angle_d0.87971987
X-RAY DIFFRACTIONf_chiral_restr0.0604207
X-RAY DIFFRACTIONf_plane_restr0.0051258
X-RAY DIFFRACTIONf_dihedral_angle_d26.5407560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-2.030.38441390.31112380X-RAY DIFFRACTION80.12
2.03-2.220.28661180.2452521X-RAY DIFFRACTION87.41
2.27-2.550.30911440.22522556X-RAY DIFFRACTION99.96
2.55-3.210.3161460.22222808X-RAY DIFFRACTION92.98
3.22-39.830.2371780.17413073X-RAY DIFFRACTION99.66

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