|Entry||Database: EMDB / ID: EMD-3325|
|Title||p97 in the ATPyS state C6 symmetrized|
|Sample||Full-length human p97|
|Keywords||AAA-ATPase / Cdc48 / Cryo-EM / ERAD / Protein quality control|
|Function / homology|
Function and homology information
flavin adenine dinucleotide catabolic process / positive regulation of Lys63-specific deubiquitinase activity / positive regulation of protein K63-linked deubiquitination / protein-DNA covalent cross-linking repair / ATPase complex / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / deubiquitinase activator activity / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion ...flavin adenine dinucleotide catabolic process / positive regulation of Lys63-specific deubiquitinase activity / positive regulation of protein K63-linked deubiquitination / protein-DNA covalent cross-linking repair / ATPase complex / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / deubiquitinase activator activity / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion / endoplasmic reticulum stress-induced pre-emptive quality control / Derlin-1 retrotranslocation complex / BAT3 complex binding / ERAD pathway / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / NADH metabolic process / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / ER-associated misfolded protein catabolic process / K48-linked polyubiquitin modification-dependent protein binding / stress granule disassembly / positive regulation of mitochondrial membrane potential / retrograde protein transport, ER to cytosol / autophagosome maturation / regulation of aerobic respiration / MHC class I protein binding / regulation of synapse organization / positive regulation of ATP biosynthetic process / negative regulation of smoothened signaling pathway / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / ATP metabolic process / RHOH GTPase cycle / Attachment and Entry / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / endoplasmic reticulum to Golgi vesicle-mediated transport / Protein methylation / translesion synthesis / HSF1 activation / proteasome complex / interstrand cross-link repair / endoplasmic reticulum unfolded protein response / lipid droplet / ubiquitin-dependent ERAD pathway / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / macroautophagy / ADP binding / Hh mutants are degraded by ERAD / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / Translesion Synthesis by POLH / ABC-family proteins mediated transport / positive regulation of protein catabolic process / positive regulation of protein-containing complex assembly / double-strand break repair / establishment of protein localization / Aggrephagy / cytoplasmic stress granule / autophagy / positive regulation of canonical Wnt signaling pathway / azurophil granule lumen / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / viral genome replication / Ovarian tumor domain proteases / Attachment and Entry / E3 ubiquitin ligases ubiquitinate target proteins / proteasome-mediated ubiquitin-dependent protein catabolic process / cellular response to heat / secretory granule lumen / protein phosphatase binding / regulation of apoptotic process / protein ubiquitination / ficolin-1-rich granule lumen / lipid binding / : / glutamatergic synapse / DNA repair / protein domain specific binding / intracellular membrane-bounded organelle / cellular response to DNA damage stimulus / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Vps4 oligomerisation, C-terminal / Vps4 C terminal oligomerisation domain ...AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Vps4 oligomerisation, C-terminal / Vps4 C terminal oligomerisation domain / Aspartate decarboxylase-like domain superfamily / AAA+ lid domain / AAA ATPase, AAA+ lid domain / AAA-protein family signature. / ATPase, AAA-type, conserved site / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transitional endoplasmic reticulum ATPase
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 6.1 Å|
|Authors||Schuller JM / Beck F / Loessl P / Heck Albert JR / Foerster F|
|Citation||Journal: FEBS Lett / Year: 2016|
Title: Nucleotide-dependent conformational changes of the AAA+ ATPase p97 revisited.
Authors: Jan M Schuller / Florian Beck / Philip Lössl / Albert J R Heck / Friedrich Förster /
Abstract: The ubiquitous AAA-ATPase p97 segregates ubiquitylated proteins from their molecular environment. Previous studies of the nucleotide-dependent conformational changes of p97 were inconclusive. Here, ...The ubiquitous AAA-ATPase p97 segregates ubiquitylated proteins from their molecular environment. Previous studies of the nucleotide-dependent conformational changes of p97 were inconclusive. Here, we determined its structure in the presence of ADP, AMP-PNP, or ATP-γS at 6.1-7.4 Å resolution using single particle cryo-electron microscopy. Both AAA domains, D1 and D2, assemble into essentially six-fold symmetrical rings. The pore of the D1-ring remains essentially closed under all nucleotide conditions, whereas the D2-ring shows an iris-like opening for ADP. The largest conformational changes of p97 are 'swinging motions' of the N-terminal domains, which may enable segregation of ubiquitylated substrates from their environment.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_3325.map.gz / Format: CCP4 / Size: 25.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.74 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Full-length human p97
|Entire||Name: Full-length human p97 / Details: p97/VCP Transitional endoplasmic reticulum ATPase / Number of Components: 1 / Oligomeric State: Homohexamer|
|Mass||Experimental: 548.491 kDa / Measured by: Native Mass-spec|
-Component #1: protein, p97/VCP Transitional endoplasmic reticulum ATPase
|Protein||Name: p97/VCP Transitional endoplasmic reticulum ATPase / a.k.a: p97 / Oligomeric Details: Homohexamer / Recombinant expression: Yes|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli (E. coli) / Vector: pQE15 / Strain: M15|
|External references||UniProt: Transitional endoplasmic reticulum ATPase|
|Specimen||Specimen State: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.8 mg/mL|
Buffer solution: Buffer: 40 mM Tris, 150 mM NaCl, 1 mM MgCl2
|Support film||Lacey Carbon grids|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen Name: ETHANE / Temperature: 120 K / Humidity: 90 % / Method: Blot for 2 seconds before plunging|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS / Date: Nov 3, 2014|
|Electron gun||Electron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 40 e/Å2 / Illumination Mode: FLOOD BEAM|
|Lens||Magnification: 105000 X (nominal)|
Astigmatism: Objective lens astigmatism was corrected at 105,000 times magnification
Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm / Energy Filter: GIF Quantum / Energy Window: 0-20 eV
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of Digital Images: 1728 |
Details: Every image is the average of 30 frames recorded by the direct electron detector
|Processing||Method: single particle reconstruction / Applied Symmetry: C6 (6 fold cyclic) / Number of Projections: 40000 |
Details: The particles were selected using an automatic selection program implemented in the TOM toolbox.
|3D reconstruction||Algorithm: Projection Matching / Software: RELION / CTF correction: On the micrograph level / Details: Map was corrected using a B-factor of -455 A^2. / Resolution: 6.1 Å / Resolution Method: FSC 0.143, gold-standard|
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