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Yorodumi- PDB-7u4z: The ubiquitin-associated domain of human thirty-eight negative ki... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7u4z | ||||||
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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 very low 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 / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Nawarathnage, S. / Smith, 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 | 7u4z.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u4z.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 7u4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/7u4z ftp://data.pdbj.org/pub/pdb/validation_reports/u4/7u4z | HTTPS FTP |
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-Related structure data
Related structure data | 7t8jC 7tcySC 7tdyC 7u4wC 2qarS S: Starting model for refinement C: citing same article (ref.) |
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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: Chemical | ChemComp-K / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.2 uL of 0.5 mg/mL protein combined with 1.2 uL of 100 mM Bis-Tris, pH 6.00, 630-750 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: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2021 |
Radiation | Monochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→33.69 Å / Num. obs: 8862 / % possible obs: 89.42 % / Redundancy: 19.5 % / Biso Wilson estimate: 27.16 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.2204 / Rpim(I) all: 0.05108 / Rrim(I) all: 0.2264 / Net I/σ(I): 11.07 |
Reflection shell | Resolution: 2.03→2.103 Å / Redundancy: 20.2 % / Rmerge(I) obs: 1.842 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 976 / CC1/2: 0.839 / CC star: 0.955 / Rpim(I) all: 0.4189 / Rrim(I) all: 1.89 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QAR, 7TCY Resolution: 2.03→33.69 Å / SU ML: 0.2118 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.2631 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: 33.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→33.69 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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