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Open data
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Basic information
| Entry | Database: PDB / ID: 4kln | ||||||
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| Title | Structure of p97 N-D1 A232E mutant in complex with ATPgS | ||||||
Components | Transitional endoplasmic reticulum ATPase | ||||||
Keywords | HYDROLASE / Transport protein | ||||||
| Function / homology | Function and homology informationcytoplasmic ubiquitin ligase complex / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / BAT3 complex binding / cellular response to arsenite ion / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination ...cytoplasmic ubiquitin ligase complex / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / BAT3 complex binding / cellular response to arsenite ion / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / cytoplasm protein quality control / positive regulation of oxidative phosphorylation / aggresome assembly / deubiquitinase activator activity / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / mitotic spindle disassembly / cellular response to misfolded protein / VCP-NPL4-UFD1 AAA ATPase complex / ciliary transition zone / positive regulation of mitochondrial membrane potential / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / stress granule disassembly / NAD+ metabolic process / ATPase complex / regulation of synapse organization / ubiquitin-specific protease binding / ciliary tip / positive regulation of ATP biosynthetic process / MHC class I protein binding / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of hippo signaling / HSF1 activation / interstrand cross-link repair / ATP metabolic process / translesion synthesis / endoplasmic reticulum unfolded protein response / proteasomal protein catabolic process / negative regulation of protein localization to chromatin / Attachment and Entry / Protein methylation / ERAD pathway / lipid droplet / proteasome complex / viral genome replication / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / macroautophagy / negative regulation of smoothened signaling pathway / establishment of protein localization / Hh mutants are degraded by ERAD / positive regulation of protein-containing complex assembly / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / positive regulation of non-canonical NF-kappaB signal transduction / Translesion Synthesis by POLH / ADP binding / autophagy / ABC-family proteins mediated transport / cytoplasmic stress granule / Aggrephagy / azurophil granule lumen / positive regulation of protein catabolic process / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / positive regulation of canonical Wnt signaling pathway / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / cellular response to heat / site of double-strand break / Neddylation / secretory granule lumen / regulation of apoptotic process / protein phosphatase binding / ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / Attachment and Entry / ciliary basal body / protein ubiquitination / intracellular membrane-bounded organelle / protein domain specific binding / DNA repair / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / lipid binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum / ATP hydrolysis activity Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Xia, D. / Tang, W.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013Title: Altered Intersubunit Communication Is the Molecular Basis for Functional Defects of Pathogenic p97 Mutants. Authors: Tang, W.K. / Xia, D. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4kln.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb4kln.ent.gz | 894.9 KB | Display | PDB format |
| PDBx/mmJSON format | 4kln.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/4kln ftp://data.pdbj.org/pub/pdb/validation_reports/kl/4kln | HTTPS FTP |
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-Related structure data
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS oper:
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Components
| #1: Protein | Mass: 54639.344 Da / Num. of mol.: 6 / Fragment: UNP residue 1-481 / Mutation: A232E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: human / Gene: p97, VCP / Plasmid: pQE60 / Production host: ![]() #2: Chemical | ChemComp-AGS / #3: Chemical | ChemComp-MG / #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: 3.15 Å3/Da / Density % sol: 60.91 % |
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| Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 0.1M citrate, pH 5.8, 0.3M NaCl, 13.6% PEG 3350, 20% glycerol, 0.525% benzamidine, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
| Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 7, 2010 |
| Radiation | Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
| Reflection | Resolution: 2.6→100 Å / Num. obs: 99906 / % possible obs: 83.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
| Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 71.8 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→46.29 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.925 / SU B: 43.205 / SU ML: 0.377 / Cross valid method: THROUGHOUT / ESU R: 1.222 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 90.242 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.62→46.29 Å
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Homo sapiens (human)
X-RAY DIFFRACTION
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