+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2591 | |||||||||
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Title | Inter-ring rotations of AAA ATPase p97 | |||||||||
Map data | reconstruction of p97 in presence of ATP-gammaS, conformation 1 | |||||||||
Sample |
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Keywords | AAA ATPase / p97 | |||||||||
Function / homology | Function and homology information RHOH GTPase cycle / HSF1 activation / Protein methylation / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / KEAP1-NFE2L2 pathway / ABC-family proteins mediated transport ...RHOH GTPase cycle / HSF1 activation / Protein methylation / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / KEAP1-NFE2L2 pathway / ABC-family proteins mediated transport / Neddylation / flavin adenine dinucleotide catabolic process / positive regulation of ubiquitin-dependent protein 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 / 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 / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / MHC class I protein binding / autophagosome maturation / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / ERAD pathway / ATP metabolic process / negative regulation of smoothened signaling pathway / Neutrophil degranulation / proteasome complex / viral genome replication / lipid droplet / macroautophagy / positive regulation of protein-containing complex assembly / positive regulation of non-canonical NF-kappaB signal transduction / ADP binding / autophagy / cytoplasmic stress granule / positive regulation of canonical Wnt signaling pathway / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / site of double-strand break / cellular response to heat / protein phosphatase binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / protein domain specific binding / DNA repair / DNA damage response / ubiquitin protein ligase binding / lipid binding / glutamatergic synapse / synapse / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 20.0 Å | |||||||||
Authors | Yeung HO / Forster A / Bebeacua C / Niwa H / Ewens C / McKeown C / Zhang X / Freemont PS | |||||||||
Citation | Journal: Open Biol / Year: 2014 Title: Inter-ring rotations of AAA ATPase p97 revealed by electron cryomicroscopy. Authors: Heidi O Yeung / Andreas Förster / Cecilia Bebeacua / Hajime Niwa / Caroline Ewens / Ciarán McKeown / Xiaodong Zhang / Paul S Freemont / Abstract: The type II AAA+ protein p97 is involved in numerous cellular activities, including endoplasmic reticulum-associated degradation, transcription activation, membrane fusion and cell-cycle control. ...The type II AAA+ protein p97 is involved in numerous cellular activities, including endoplasmic reticulum-associated degradation, transcription activation, membrane fusion and cell-cycle control. These activities are at least in part regulated by the ubiquitin system, in which p97 is thought to target ubiquitylated protein substrates within macromolecular complexes and assist in their extraction or disassembly. Although ATPase activity is essential for p97 function, little is known about how ATP binding or hydrolysis is coupled with p97 conformational changes and substrate remodelling. Here, we have used single-particle electron cryomicroscopy (cryo-EM) to study the effect of nucleotides on p97 conformation. We have identified conformational heterogeneity within the cryo-EM datasets from which we have resolved two major p97 conformations. A comparison of conformations reveals inter-ring rotations upon nucleotide binding and hydrolysis that may be linked to the remodelling of target protein complexes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2591.map.gz | 366.8 KB | EMDB map data format | |
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Header (meta data) | emd-2591-v30.xml emd-2591.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_2591.jpg | 48 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2591 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2591 | HTTPS FTP |
-Validation report
Summary document | emd_2591_validation.pdf.gz | 191.4 KB | Display | EMDB validaton report |
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Full document | emd_2591_full_validation.pdf.gz | 190.5 KB | Display | |
Data in XML | emd_2591_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2591 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2591 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2591.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | reconstruction of p97 in presence of ATP-gammaS, conformation 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.53 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : p97 in presence of ATP-gammaS, conformation 1
Entire | Name: p97 in presence of ATP-gammaS, conformation 1 |
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Components |
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-Supramolecule #1000: p97 in presence of ATP-gammaS, conformation 1
Supramolecule | Name: p97 in presence of ATP-gammaS, conformation 1 / type: sample / ID: 1000 / Details: p97 E578Q mutant comprising residues 22-806 / Oligomeric state: homohexamer / Number unique components: 1 |
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Molecular weight | Theoretical: 550 KDa |
-Macromolecule #1: Transitional endoplasmic reticulum ATPase
Macromolecule | Name: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 1 / Name.synonym: VCP, P97 / Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: House mouse |
Molecular weight | Theoretical: 90 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pET28 |
Sequence | UniProtKB: Transitional endoplasmic reticulum ATPase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.8 mg/mL |
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Buffer | pH: 8 / Details: 250 mM NaCl, 25 mM Tris, 2.5 mM MgCl2 |
Grid | Details: carbon film on copper grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II / Method: Blot for two seconds before plunging. |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Date | May 10, 2008 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm |
Sample stage | Specimen holder model: GATAN HELIUM |
-Image processing
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: Imagic / Number images used: 46600 |
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Final two d classification | Number classes: 2 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C |
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Software | Name: VEDA |
Details | N, D1 and D2 domains fitted separately under imposition of sixfold symmetry |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient |
-Atomic model buiding 2
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: VEDA |
Details | N, D1 and D2 domains fitted separately under imposition of sixfold symmetry |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient |