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- PDB-7zk2: Crystal Structure of human Brachyury G177D variant in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7zk2
TitleCrystal Structure of human Brachyury G177D variant in complex with CSC027898502
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 / 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-IU4 / PHOSPHATE ION / T-box transcription factor T
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 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: To Be Published
Title: Crystal Structure of human Brachyury G177D variant in complex with CSC027898502
Authors: Newman, J.A. / Gavard, A. / Aitkenhead, H. / Imprachim, N. / Sherestha, L. / Burgess-Brown, N.A. / von Delft, F. / Bountra, C. / Gileadi, O.
History
DepositionApr 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release

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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)20,0543
Polymers19,6561
Non-polymers3982
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-5 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.920, 99.920, 98.680
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-773-

HOH

21A-843-

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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-IU4 / N-[4-(2-morpholin-4-yl-1,3-thiazol-4-yl)phenyl]ethanamide


Mass: 303.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / 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: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→39.63 Å / Num. obs: 25137 / % possible obs: 99.73 % / Redundancy: 16 % / Biso Wilson estimate: 25.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1238 / Rpim(I) all: 0.03021 / Net I/σ(I): 11.83
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 2.721 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 2476 / CC1/2: 0.374

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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: 1.6→39.63 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 1239 4.94 %
Rwork0.2058 --
obs0.2072 25072 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 26 215 1621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091479
X-RAY DIFFRACTIONf_angle_d0.982010
X-RAY DIFFRACTIONf_dihedral_angle_d31.21211
X-RAY DIFFRACTIONf_chiral_restr0.065207
X-RAY DIFFRACTIONf_plane_restr0.007262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.660.33321370.31472629X-RAY DIFFRACTION100
1.66-1.740.30281410.28222615X-RAY DIFFRACTION100
1.74-1.830.30071290.27222632X-RAY DIFFRACTION100
1.83-1.950.35341570.25992611X-RAY DIFFRACTION100
1.95-2.10.27391510.23272630X-RAY DIFFRACTION100
2.1-2.310.30471330.22012655X-RAY DIFFRACTION100
2.31-2.640.24991130.21962666X-RAY DIFFRACTION100
2.64-3.330.21821320.21012655X-RAY DIFFRACTION99
3.33-39.630.18351460.1692740X-RAY DIFFRACTION100

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