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Yorodumi- PDB-6iwd: The PTP domain of human PTPN14 in a complex with the CR3 domain o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iwd | ||||||
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Title | The PTP domain of human PTPN14 in a complex with the CR3 domain of HPV18 E7 | ||||||
Components |
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Keywords | ONCOPROTEIN | ||||||
Function / homology | Function and homology information lymphangiogenesis / Interleukin-37 signaling / regulation of protein export from nucleus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / transcription coregulator activity / receptor tyrosine kinase binding / host cell cytoplasm ...lymphangiogenesis / Interleukin-37 signaling / regulation of protein export from nucleus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / transcription coregulator activity / receptor tyrosine kinase binding / host cell cytoplasm / cytoskeleton / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of cell population proliferation / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human papillomavirus type 18 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yun, H.-Y. / Kim, S.J. / Ku, B. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Plos Biol. / Year: 2019 Title: Structural basis for recognition of the tumor suppressor protein PTPN14 by the oncoprotein E7 of human papillomavirus. Authors: Yun, H.Y. / Kim, M.W. / Lee, H.S. / Kim, W. / Shin, J.H. / Kim, H. / Shin, H.C. / Park, H. / Oh, B.H. / Kim, W.K. / Bae, K.H. / Lee, S.C. / Lee, E.W. / Ku, B. / Kim, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iwd.cif.gz | 91.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iwd.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 6iwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iwd_validation.pdf.gz | 456.4 KB | Display | wwPDB validaton report |
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Full document | 6iwd_full_validation.pdf.gz | 457.9 KB | Display | |
Data in XML | 6iwd_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 6iwd_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/6iwd ftp://data.pdbj.org/pub/pdb/validation_reports/iw/6iwd | HTTPS FTP |
-Related structure data
Related structure data | 2bzlS 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 on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 35063.305 Da / Num. of mol.: 1 / Fragment: UNP residues 886-1187 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15678, protein-tyrosine-phosphatase |
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#2: Protein | Mass: 6283.309 Da / Num. of mol.: 1 / Fragment: UNP residues 54-105 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human papillomavirus type 18 / Gene: E7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q76Z96, UniProt: P06788*PLUS |
-Non-polymers , 4 types, 272 molecules
#3: Chemical | ChemComp-CL / | ||||
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#4: Chemical | #5: Chemical | ChemComp-ZN / | #6: 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: 2.37 Å3/Da / Density % sol: 48.19 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris-HCl pH 8.0, 25% (w/v) polyethylene glycol 3350, 0.25 M lithium sulfate monohydrate, and 2% (v/v) tert-butanol |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 35719 / % possible obs: 95.1 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 41.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.328 / Num. unique obs: 1615 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BZL Resolution: 1.8→29.987 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 21.57
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.987 Å
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Refine LS restraints |
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LS refinement shell |
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