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Yorodumi- PDB-7u4w: The ubiquitin-associated domain of human thirty-eight negative ki... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7u4w | ||||||
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Title | The ubiquitin-associated domain of human thirty-eight negative kinase-1 flexibly fused to the 1TEL crystallization chaperone via a 2-glycine linker and crystallized at traditional protein concentration | ||||||
Components | Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1 | ||||||
Keywords | SIGNALING PROTEIN / Protein polymer / Ubiquitin-associated domain / Helix bundle / Chimera | ||||||
Function / homology | Function and homology information Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / DNA-binding transcription repressor activity, RNA polymerase II-specific ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / protein tyrosine kinase activity / protein autophosphorylation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / protein phosphorylation / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Nawarathnage, S. / Pedroza Romo, M.J. / Smith, T. / Bunn, D. / Stewart, C. / Doukov, T. / Moody, J.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2023 Title: Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain. Authors: Nawarathnage, S. / Tseng, Y.J. / Soleimani, S. / Smith, T. / Pedroza Romo, M.J. / Abiodun, W.O. / Egbert, C.M. / Madhusanka, D. / Bunn, D. / Woods, B. / Tsubaki, E. / Stewart, C. / Brown, S. ...Authors: Nawarathnage, S. / Tseng, Y.J. / Soleimani, S. / Smith, T. / Pedroza Romo, M.J. / Abiodun, W.O. / Egbert, C.M. / Madhusanka, D. / Bunn, D. / Woods, B. / Tsubaki, E. / Stewart, C. / Brown, S. / Doukov, T. / Andersen, J.L. / Moody, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u4w.cif.gz | 76.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u4w.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 7u4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u4w_validation.pdf.gz | 417.4 KB | Display | wwPDB validaton report |
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Full document | 7u4w_full_validation.pdf.gz | 417.6 KB | Display | |
Data in XML | 7u4w_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 7u4w_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/7u4w ftp://data.pdbj.org/pub/pdb/validation_reports/u4/7u4w | HTTPS FTP |
-Related structure data
Related structure data | 7t8jC 7tcyC 7tdyC 7u4zC 1telS 2qarS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17775.053 Da / Num. of mol.: 1 / Mutation: R80S,V112E,C610A,C644A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, TNK1 / Plasmid: pET42_SUMO / Details (production host): N-term cleavable 10xHis / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B References: UniProt: P41212, UniProt: Q13470, non-specific protein-tyrosine kinase |
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#2: 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: 2.09 Å3/Da / Density % sol: 41.19 % / Description: Tapered hexagonal prisms |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.2 uL of 15 mg/mL protein combined with 1.2 uL of 100 mM Bis-Tris, pH 6.50, 750 mM Mg-Formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2020 |
Radiation | Monochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40.48 Å / Num. obs: 8522 / % possible obs: 98.32 % / Redundancy: 14.5 % / Biso Wilson estimate: 51.29 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04076 / Rpim(I) all: 0.01108 / Rrim(I) all: 0.04229 / Net I/σ(I): 28.14 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.088 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 820 / CC1/2: 0.923 / CC star: 0.98 / Rpim(I) all: 0.2973 / Rrim(I) all: 1.129 / % possible all: 96.24 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QAR (for 1TEL), homology model (UBA) Resolution: 2.1→40.48 Å / SU ML: 0.3045 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.1723 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: 72.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→40.48 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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