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Yorodumi- PDB-8cdn: Crystal structure of human Brachyury in complex with a single T b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cdn | ||||||
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Title | Crystal structure of human Brachyury in complex with a single T box binding element DNA | ||||||
Components |
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Keywords | TRANSCRIPTION / Brachyury / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Newman, J.A. / Gavard, A.E. / von Delft, F. / Gileadi, O. / Bountra, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of human Brachyury in complex with a single T box binding element DNA Authors: Newman, J.A. / Gavard, A.E. / von Delft, F. / Gileadi, O. / Bountra, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cdn.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cdn.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 8cdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/8cdn ftp://data.pdbj.org/pub/pdb/validation_reports/cd/8cdn | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22022.357 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 |
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#2: DNA chain | Mass: 3718.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: DNA chain | Mass: 3607.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.38 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop Details: 0.1M ammonium acetate -- 0.1M bis-tris pH 5.5 -- 16%(w/v) PEG10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→109 Å / Num. obs: 9158 / % possible obs: 100 % / Redundancy: 17.4 % / Biso Wilson estimate: 72.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.111 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.55→2.62 Å / Rmerge(I) obs: 2.863 / Mean I/σ(I) obs: 1 / Num. unique obs: 666 / CC1/2: 0.593 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→54.57 Å / SU ML: 0.326 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 35.7359 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→54.57 Å
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Refine LS restraints |
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LS refinement shell |
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