+Open data
-Basic information
Entry | Database: PDB / ID: 7l5x | ||||||
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Title | p97-R155H mutant dodecamer II | ||||||
Components | Transitional endoplasmic reticulum ATPase | ||||||
Keywords | HYDROLASE / AAA+ ATPase / MOTOR PROTEIN | ||||||
Function / homology | Function and homology information positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / 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 Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / 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 / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / NADH metabolic process / 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 / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / MHC class I protein binding / RHOH GTPase cycle / autophagosome maturation / HSF1 activation / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / Protein methylation / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / negative regulation of smoothened signaling pathway / ERAD pathway / ATP metabolic process / endoplasmic reticulum unfolded protein response / Attachment and Entry / viral genome replication / proteasome complex / lipid droplet / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hh mutants are degraded by ERAD / macroautophagy / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / establishment of protein localization / ABC-family proteins mediated transport / ADP binding / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / site of double-strand break / cellular response to heat / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair / glutamatergic synapse / lipid binding / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / RNA binding / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.1 Å | ||||||
Authors | Nandi, P. / Li, S. / Coulmbres, R.C.A. / Wang, F. / Williams, D.R. / Malyutin, A.G. / Poh, Y.-P. / Chou, T.-F. / Chiu, P.-L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Int J Mol Sci / Year: 2021 Title: Structural and Functional Analysis of Disease-Linked p97 ATPase Mutant Complexes. Authors: Purbasha Nandi / Shan Li / Rod Carlo A Columbres / Feng Wang / Dewight R Williams / Yu-Ping Poh / Tsui-Fen Chou / Po-Lin Chiu / Abstract: IBMPFD/ALS is a genetic disorder caused by a single amino acid mutation on the p97 ATPase, promoting ATPase activity and cofactor dysregulation. The disease mechanism underlying p97 ATPase ...IBMPFD/ALS is a genetic disorder caused by a single amino acid mutation on the p97 ATPase, promoting ATPase activity and cofactor dysregulation. The disease mechanism underlying p97 ATPase malfunction remains unclear. To understand how the mutation alters the ATPase regulation, we assembled a full-length p97 with its p47 cofactor and first visualized their structures using single-particle cryo-EM. More than one-third of the population was the dodecameric form. Nucleotide presence dissociates the dodecamer into two hexamers for its highly elevated function. The N-domains of the p97 mutant all show up configurations in ADP- or ATPS-bound states. Our functional and structural analyses showed that the p47 binding is likely to impact the p97 ATPase activities via changing the conformations of arginine fingers. These functional and structural analyses underline the ATPase dysregulation with the miscommunication between the functional modules of the p97. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7l5x.cif.gz | 868.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l5x.ent.gz | 624 KB | Display | PDB format |
PDBx/mmJSON format | 7l5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7l5x_validation.pdf.gz | 937.8 KB | Display | wwPDB validaton report |
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Full document | 7l5x_full_validation.pdf.gz | 945.9 KB | Display | |
Data in XML | 7l5x_validation.xml.gz | 114.7 KB | Display | |
Data in CIF | 7l5x_validation.cif.gz | 197.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/7l5x ftp://data.pdbj.org/pub/pdb/validation_reports/l5/7l5x | HTTPS FTP |
-Related structure data
Related structure data | 23192MC 7l5wC 7r7sC 7r7tC 7r7uC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 89417.773 Da / Num. of mol.: 12 / Mutation: R155H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P55072, vesicle-fusing ATPase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: p97-R155H disease mutant / Type: COMPLEX / Details: p97-R155H dodecamer II / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 1.071 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia virus LL11 / Strain: BL21 | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The protein sample was monodisperse. | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/1 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 292 K / Details: The grid was blotted for 6 seconds. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 48077 X / Nominal defocus max: -2500 nm / Nominal defocus min: -800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Residual tilt: 0.001 mradians |
Image recording | Electron dose: 44.4 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3512 |
Image scans | Sampling size: 5 µm |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1124232 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D6 (2x6 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2219 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 183.2 / Protocol: OTHER / Space: REAL / Target criteria: CC | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5FTK Accession code: 5FTK / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
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