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Yorodumi- PDB-9cpl: The ubiquitin-associated domain of human thirty-eight negative ki... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9cpl | ||||||
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Title | The ubiquitin-associated domain of human thirty-eight negative kinase 1, fused to the 2TEL crystallization chaperone via a 2-glycine linker | ||||||
Components | 2TEL/Non-receptor tyrosine-protein kinase TNK1 fusion protein | ||||||
Keywords | ONCOPROTEIN / TELSAM / 2TEL / Pointed Domain / ETS / TEL / TNK1 / UBA Domain / Broken Periodicity | ||||||
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 / protein tyrosine kinase activity / DNA-binding transcription activator activity, RNA polymerase II-specific / protein autophosphorylation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein phosphorylation / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / 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: 2.4 Å | ||||||
Authors | Samarawickrama, P. / Averett, J. / Doukov, T. / Moody, J.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: 1TEL Fusions Outperform 2TEL and 3TEL Fusions in Controlled Comparisons Authors: Samarawickrama, P. / Ludlow, K. / Probst, R. / Abiodun, W. / Averett, J. / Hansen, D. / Doukov, T. / 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 | 9cpl.cif.gz | 118.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9cpl.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 9cpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9cpl_validation.pdf.gz | 683.2 KB | Display | wwPDB validaton report |
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Full document | 9cpl_full_validation.pdf.gz | 683.7 KB | Display | |
Data in XML | 9cpl_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 9cpl_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/9cpl ftp://data.pdbj.org/pub/pdb/validation_reports/cp/9cpl | HTTPS FTP |
-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: 29092.832 Da / Num. of mol.: 1 Mutation: First TELSAM:R80S,V112E,Second TELSAM: R80S,UBA Domain: C610A,C644A Source method: isolated from a genetically manipulated source Details: Tandem fusion of Two TELSAM Domains followed by TNK1 domain Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, TNK1 / Plasmid: pET42-His-2TEL-XhoI / Details (production host): N-term 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-FMT / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.48 % / Description: clusters of rice-shaped crystals |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100mM BisTris, pH 6.0, 960mM 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: Aug 25, 2023 / Details: Rh coated collimating mirror, K-B focusing mirrors |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal monochromator, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.78 Å / Num. obs: 12862 / % possible obs: 99.12 % / Redundancy: 10.2 % / Biso Wilson estimate: 68.73 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1028 / Rpim(I) all: 0.03386 / Rrim(I) all: 0.1083 / Net I/σ(I): 10.88 |
Reflection shell | Resolution: 2.4→2.4 Å / Redundancy: 10.2 % / Rmerge(I) obs: 3.597 / Mean I/σ(I) obs: 0.62 / Num. unique obs: 1150 / CC1/2: 0.449 / CC star: 0.787 / Rpim(I) all: 1.173 / Rrim(I) all: 3.786 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.78 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3038 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→45.78 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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