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Yorodumi- PDB-5ifw: Quantitative interaction mapping reveals an extended ubiquitin re... -
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-Basic information
Entry | Database: PDB / ID: 5ifw | ||||||
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Title | Quantitative interaction mapping reveals an extended ubiquitin regulatory domain in ASPL that disrupts functional p97 hexamers and induces cell death | ||||||
Components |
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Keywords | SIGNALING PROTEIN / ASPL / p97 / disassembly / hexamer / eUBX | ||||||
Function / homology | Function and homology information positive regulation of protein modification process / regulation of glucose import / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / vesicle membrane / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway ...positive regulation of protein modification process / regulation of glucose import / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / vesicle membrane / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / aggresome assembly / NADH metabolic process / regulation of protein localization to chromatin / vesicle-fusing ATPase / cellular response to misfolded protein / : / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / ERAD pathway / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / ATPase complex / regulation of synapse organization / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / autophagosome maturation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / HSF1 activation / endomembrane system / translesion synthesis / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class I protein binding / Protein methylation / interstrand cross-link repair / negative regulation of smoothened signaling pathway / ATP metabolic process / : / Attachment and Entry / endoplasmic reticulum unfolded protein response / endoplasmic reticulum-Golgi intermediate compartment membrane / lipid droplet / proteasome complex / viral genome replication / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Translocation of SLC2A4 (GLUT4) to the plasma membrane / proteasomal protein catabolic process / Hh mutants are degraded by ERAD / positive regulation of protein-containing complex assembly / ADP binding / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / macroautophagy / intracellular protein transport / Translesion Synthesis by POLH / ABC-family proteins mediated transport / establishment of protein localization / cytoplasmic side of plasma membrane / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / azurophil granule lumen / KEAP1-NFE2L2 pathway / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / glucose homeostasis / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / cellular response to heat / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein phosphatase binding / secretory granule lumen / regulation of apoptotic process / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair / glutamatergic synapse / lipid binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å | ||||||
Authors | Roske, Y. / Heinemann, U. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Quantitative interaction mapping reveals an extended UBX domain in ASPL that disrupts functional p97 hexamers. Authors: Arumughan, A. / Roske, Y. / Barth, C. / Forero, L.L. / Bravo-Rodriguez, K. / Redel, A. / Kostova, S. / McShane, E. / Opitz, R. / Faelber, K. / Rau, K. / Mielke, T. / Daumke, O. / Selbach, M. ...Authors: Arumughan, A. / Roske, Y. / Barth, C. / Forero, L.L. / Bravo-Rodriguez, K. / Redel, A. / Kostova, S. / McShane, E. / Opitz, R. / Faelber, K. / Rau, K. / Mielke, T. / Daumke, O. / Selbach, M. / Sanchez-Garcia, E. / Rocks, O. / Panakova, D. / Heinemann, U. / Wanker, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ifw.cif.gz | 192.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ifw.ent.gz | 148.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ifw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/5ifw ftp://data.pdbj.org/pub/pdb/validation_reports/if/5ifw | HTTPS FTP |
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-Related structure data
Related structure data | 5ifsC 3cf1S S: Starting model for refinement C: citing same article (ref.) |
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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: 21356.389 Da / Num. of mol.: 1 / Fragment: UNP residues 317-504 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ASPSCR1, ASPL, RCC17, TUG, UBXD9, UBXN9 / Plasmid: pQLinkG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q9BZE9 | ||
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#2: Protein | Mass: 89449.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Plasmid: pQLinkG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: P55072, vesicle-fusing ATPase | ||
#3: Chemical | #4: 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: 3.54 Å3/Da / Density % sol: 65.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.4→33.9 Å / Num. obs: 20794 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 56.207 Å2 / Rmerge(I) obs: 0.168 / Net I/σ(I): 10.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CF1 Resolution: 3.4→33.887 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 25.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→33.887 Å
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Refine LS restraints |
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LS refinement shell |
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