+Open data
-Basic information
Entry | Database: PDB / ID: 3iv1 | ||||||
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Title | Coiled-coil domain of tumor susceptibility gene 101 | ||||||
Components | Tumor susceptibility gene 101 proteinTSG101 | ||||||
Keywords | HYDROLASE / COILED_COIL / TUMORIGENESIS / CELL_CYCLE REGULATION / Alternative splicing / Cell cycle / Cell division / Coiled coil / Cytoplasm / Endosome / Growth regulation / Host-virus interaction / Membrane / Nucleus / Phosphoprotein / Polymorphism / Protein transport / Transport / Ubl conjugation / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ...positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / membrane fission / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / Flemming body / virion binding / endosome to lysosome transport / negative regulation of epidermal growth factor receptor signaling pathway / viral budding via host ESCRT complex / autophagosome maturation / viral release from host cell / keratinocyte differentiation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / HCMV Late Events / ubiquitin binding / regulation of cell growth / macroautophagy / Late endosomal microautophagy / protein modification process / Budding and maturation of HIV virion / transcription corepressor activity / calcium-dependent protein binding / late endosome / late endosome membrane / early endosome membrane / early endosome / endosome membrane / regulation of cell cycle / endosome / cell cycle / cell division / negative regulation of cell population proliferation / centrosome / ubiquitin protein ligase binding / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / extracellular exosome / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Neculai, D. / Avvakumov, G.V. / Wernimont, A.K. / Xue, S. / Walker, J.R. / Li, Y. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. ...Neculai, D. / Avvakumov, G.V. / Wernimont, A.K. / Xue, S. / Walker, J.R. / Li, Y. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Coiled-Coil Domain of Human Tsg101 Authors: Neculai, D. / Avvakumov, G.V. / Wernimont, A.K. / Xue, S. / Walker, J.R. / Li, Y. / Weigelt, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iv1.cif.gz | 254.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iv1.ent.gz | 220.3 KB | Display | PDB format |
PDBx/mmJSON format | 3iv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/3iv1 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/3iv1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 9198.006 Da / Num. of mol.: 8 / Fragment: COILED-COIL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TSG101 / Plasmid: PET28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99816 #2: Chemical | ChemComp-SO4 / | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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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: 2.12 Å3/Da / Density % sol: 42.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2.4 M AMMONIUM SULFATE, 0.1 M BIS-TRIS, 1 mM DTT, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2009 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 25250 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.77 % / Biso Wilson estimate: 40.91 Å2 / Rsym value: 0.071 / Net I/σ(I): 14.87 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 3.66 % / Mean I/σ(I) obs: 7.78 / Rsym value: 0.16 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→48.75 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.329 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→48.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.65 Å / Total num. of bins used: 13
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