+Open data
-Basic information
Entry | Database: PDB / ID: 5to7 | ||||||
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Title | Structure of the TPR oligomerization domain | ||||||
Components | Nucleoprotein TPR | ||||||
Keywords | CELL CYCLE / TPR oligomerization domain / Receptor tyrosine kinase / MET / Oncogenic Fusion kinases | ||||||
Function / homology | Function and homology information regulation of mitotic sister chromatid separation / RNA import into nucleus / mRNA export from nucleus in response to heat stress / cellular response to interferon-alpha / negative regulation of RNA export from nucleus / positive regulation of mitotic cell cycle spindle assembly checkpoint / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / positive regulation of intracellular protein transport ...regulation of mitotic sister chromatid separation / RNA import into nucleus / mRNA export from nucleus in response to heat stress / cellular response to interferon-alpha / negative regulation of RNA export from nucleus / positive regulation of mitotic cell cycle spindle assembly checkpoint / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / positive regulation of intracellular protein transport / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / regulation of mitotic spindle assembly / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / cytoplasmic dynein complex / SUMOylation of SUMOylation proteins / response to epidermal growth factor / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / mitogen-activated protein kinase binding / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / dynein complex binding / mitotic spindle assembly checkpoint signaling / SUMOylation of ubiquitinylation proteins / positive regulation of heterochromatin formation / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA export from nucleus / nuclear pore / SUMOylation of DNA damage response and repair proteins / heat shock protein binding / negative regulation of translational initiation / tubulin binding / SUMOylation of chromatin organization proteins / nuclear periphery / positive regulation of protein export from nucleus / HCMV Late Events / Transcriptional regulation by small RNAs / mitotic spindle / kinetochore / ISG15 antiviral mechanism / positive regulation of protein import into nucleus / HCMV Early Events / protein import into nucleus / Signaling by ALK fusions and activated point mutants / nuclear envelope / regulation of protein localization / snRNP Assembly / cellular response to heat / nuclear membrane / cell division / mRNA binding / chromatin binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Pal, K. / Xu, Q. / Zhou, X.E. / Melcher, K. / Xu, H.E. | ||||||
Citation | Journal: Structure / Year: 2017 Title: Structural Basis of TPR-Mediated Oligomerization and Activation of Oncogenic Fusion Kinases. Authors: Pal, K. / Bandyopadhyay, A. / Zhou, X.E. / Xu, Q. / Marciano, D.P. / Brunzelle, J.S. / Yerrum, S. / Griffin, P.R. / Vande Woude, G. / Melcher, K. / Xu, H.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5to7.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5to7.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 5to7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5to7_validation.pdf.gz | 437 KB | Display | wwPDB validaton report |
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Full document | 5to7_full_validation.pdf.gz | 437.9 KB | Display | |
Data in XML | 5to7_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 5to7_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/5to7 ftp://data.pdbj.org/pub/pdb/validation_reports/to/5to7 | HTTPS FTP |
-Related structure data
Related structure data | 5to5C 5to6C 5tvbC 5tv5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16763.898 Da / Num. of mol.: 4 / Fragment: UNP residues 2-142 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TPR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12270 #2: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.5 % |
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 7.25 / Details: 28% PEG1K, 0.1M HEPES (7.25) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47.49 Å / Num. obs: 28341 / % possible obs: 97.5 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.3 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TV5 Resolution: 2.6→44.019 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.45
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.83 Å2 / Biso mean: 55.3081 Å2 / Biso min: 19.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→44.019 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
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