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- PDB-7zl2: Crystal Structure of human Brachyury G177D variant in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7zl2
TitleCrystal Structure of human Brachyury G177D variant in complex with Molpolrt-039-246-810
ComponentsT-box transcription factor T
KeywordsTRANSCRIPTION / TBXT / chordoma / 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 / 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
: / T-box transcription factor T
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 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 13, 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 2.0Jan 22, 2025Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._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_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.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)19,9662
Polymers19,6561
Non-polymers3101
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint0 kcal/mol
Surface area9160 Å2
Unit cell
Length a, b, c (Å)99.970, 99.970, 99.360
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-477-

HOH

21A-498-

HOH

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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-IXB / (3S)-1-(3-aminocarbonylphenyl)carbonyl-2,3-dihydroindole-3-carboxylic acid / 1-(3-carbamoylbenzoyl)-2,3-dihydro-1H-indole-3-carboxylic acid


Mass: 310.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 298 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: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→65.27 Å / Num. obs: 17841 / % possible obs: 99.87 % / Redundancy: 20.4 % / CC1/2: 0.99 / Rrim(I) all: 0.124 / Net I/σ(I): 16.5
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 873 / CC1/2: 0.7 / Rrim(I) all: 2.187 / % possible all: 100

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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: 1.8→43.09 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2726 917 5.14 %
Rwork0.2234 --
obs0.2258 17839 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→43.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 23 222 1625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021461
X-RAY DIFFRACTIONf_angle_d0.5241986
X-RAY DIFFRACTIONf_dihedral_angle_d24.965559
X-RAY DIFFRACTIONf_chiral_restr0.045207
X-RAY DIFFRACTIONf_plane_restr0.004259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.90.35431230.32732378X-RAY DIFFRACTION100
1.9-2.010.32341280.28092400X-RAY DIFFRACTION100
2.01-2.170.2781280.25072400X-RAY DIFFRACTION100
2.17-2.390.32881240.25092404X-RAY DIFFRACTION100
2.39-2.730.31521520.25022393X-RAY DIFFRACTION100
2.73-3.440.28341230.2322437X-RAY DIFFRACTION100
3.44-43.090.22541390.18362510X-RAY DIFFRACTION100

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