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- PDB-8a7n: Crystal Structure of human Brachyury G177D variant in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8a7n
TitleCrystal Structure of human Brachyury G177D variant in complex with (S)-N-(3-aminopropyl)-3-((1-(2-fluorophenyl)-2-oxopyrrolidin-3-yl)amino)-N-methylbenzamide (CF-2-125)
ComponentsT-box transcription factor T
KeywordsTRANSCRIPTION / Brachyury / Chordoma / 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 / chromatin / regulation of transcription by RNA polymerase II / 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, DNA-binding domain / T-box transcription factor / Transcription factor, T-box, conserved site / T-box superfamily / 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
Chem-L9E / PHOSPHATE ION / T-box transcription factor T
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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
Citation
Journal: To Be Published
Title: Crystal Structure of human Brachyury G177D variant in complex with (S)-N-(3-aminopropyl)-3-((1-(2-fluorophenyl)-2-oxopyrrolidin-3-yl)amino)-N-methylbenzamide (CF-2-125)
Authors: Newman, J.A. / Gavard, A. / Aitkenhead, H. / Imprachim, N. / Sherestha, L. / Burgess-Brown, N.A. / von Delft, F. / Bountra, C. / Gileadi, O.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJun 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-box transcription factor T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1353
Polymers19,6561
Non-polymers4792
Water2,666148
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-2 kcal/mol
Surface area9530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.392, 100.392, 99.194
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
Components on special symmetry positions
IDModelComponents
11A-301-

PO4

21A-438-

HOH

31A-504-

HOH

41A-542-

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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-L9E / N-(3-azanylpropyl)-3-[[(3S)-1-(2-fluorophenyl)-2-oxidanylidene-pyrrolidin-3-yl]amino]-N-methyl-benzamide / (S)-N-(3-aminopropyl)-3-((1-(2-fluorophenyl)-2-oxopyrrolidin-3-yl)amino)-N-methylbenzamide


Mass: 384.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25FN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 49.74 %
Crystal growTemperature: 277 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: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→50.2 Å / Num. obs: 15336 / % possible obs: 100 % / Redundancy: 18.4 % / Biso Wilson estimate: 32.14 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.025 / Net I/σ(I): 18
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 1.782 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 976 / CC1/2: 0.805 / Rpim(I) all: 0.581 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5QT0

5qt0


Resolution: 1.9→50.2 Å / SU ML: 0.2631 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.8488
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2364 762 4.97 %
Rwork0.1944 14559 -
obs0.1966 15321 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.07 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 33 148 1561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681490
X-RAY DIFFRACTIONf_angle_d0.9042027
X-RAY DIFFRACTIONf_chiral_restr0.0621209
X-RAY DIFFRACTIONf_plane_restr0.0057265
X-RAY DIFFRACTIONf_dihedral_angle_d26.1237574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.050.35661690.27922854X-RAY DIFFRACTION99.77
2.05-2.250.29851390.22712894X-RAY DIFFRACTION99.97
2.25-2.580.27511520.20822894X-RAY DIFFRACTION99.9
2.58-3.250.24351210.21322931X-RAY DIFFRACTION99.97
3.25-50.20.20511810.16772986X-RAY DIFFRACTION99.97

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