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- PDB-7oat: Structural basis for targeted p97 remodelling by ASPL as prerequi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7oat | ||||||
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Title | Structural basis for targeted p97 remodelling by ASPL as prerequisite for p97 trimethylation by METTL21D | ||||||
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![]() | TRANSFERASE / p97 / AAA+ ATPase / ASPL / METTL21D / VCP-KMT / VCP / methylation / remodelling | ||||||
Function / homology | ![]() peptidyl-lysine methylation / positive regulation of protein modification process / peptidyl-lysine trimethylation / regulation of glucose import / negative regulation of ATP-dependent activity / positive regulation of Lys63-specific deubiquitinase activity / protein-lysine N-methyltransferase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex ...peptidyl-lysine methylation / positive regulation of protein modification process / peptidyl-lysine trimethylation / regulation of glucose import / negative regulation of ATP-dependent activity / positive regulation of Lys63-specific deubiquitinase activity / protein-lysine N-methyltransferase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / protein-DNA covalent cross-linking repair / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / aggresome assembly / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / vesicle-fusing ATPase / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / vesicle membrane / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / histone methyltransferase activity / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / MHC class I protein binding / autophagosome maturation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / HSF1 activation / proteasomal protein catabolic process / endomembrane system / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / Protein methylation / interstrand cross-link repair / ERAD pathway / ATP metabolic process / negative regulation of smoothened signaling pathway / endoplasmic reticulum unfolded protein response / Attachment and Entry / endoplasmic reticulum-Golgi intermediate compartment membrane / proteasome complex / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / lipid droplet / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Translocation of SLC2A4 (GLUT4) to the plasma membrane / macroautophagy / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / intracellular protein transport / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / establishment of protein localization / positive regulation of non-canonical NF-kappaB signal transduction / ABC-family proteins mediated transport / cytoplasmic side of plasma membrane / activation of cysteine-type endopeptidase activity involved in apoptotic process / ADP binding / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / azurophil granule lumen / KEAP1-NFE2L2 pathway / double-strand break repair / glucose homeostasis / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / ATPase binding / Neddylation / site of double-strand break / cellular response to heat / protein phosphatase binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / regulation of apoptotic process / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Petrovic, S. / Heinemann, U. / Roske, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural remodeling of AAA+ ATPase p97 by adaptor protein ASPL facilitates posttranslational methylation by METTL21D. Authors: Petrovic, S. / Roske, Y. / Rami, B. / Phan, M.H.Q. / Panakova, D. / Heinemann, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 345.7 KB | Display | ![]() |
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PDB format | ![]() | 276.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 30.4 KB | Display | |
Data in CIF | ![]() | 41.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oasC ![]() 5ifsS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 21606.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 53506.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 25232.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9H867, Transferases; Transferring one-carbon groups; Methyltransferases |
-Non-polymers , 5 types, 65 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-ATP / | #6: Chemical | ChemComp-MG / | #7: Chemical | ChemComp-SAH / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 16% PEG 8000, 0.2 M calcium acetate, 0.1 M MES (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.995→49.32 Å / Num. obs: 20828 / % possible obs: 98.1 % / Redundancy: 6.17 % / Biso Wilson estimate: 96.23 Å2 / CC1/2: 0.986 / Rrim(I) all: 0.273 / Net I/σ(I): 6.65 |
Reflection shell | Resolution: 3→3.15 Å / Mean I/σ(I) obs: 0.79 / Num. unique obs: 3167 / CC1/2: 0.324 / Rrim(I) all: 1.983 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5IFS Resolution: 2.995→49.32 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.858 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.442
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Displacement parameters | Biso max: 139.78 Å2 / Biso mean: 78.66 Å2 / Biso min: 21.53 Å2
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Refine analyze | Luzzati coordinate error obs: 0.49 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.995→49.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.02 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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