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- EMDB-2590: Inter-ring rotations of AAA ATPase p97 -

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Basic information

Entry
Database: EMDB / ID: EMD-2590
TitleInter-ring rotations of AAA ATPase p97
Map dataReconstruction of p97 in presence of ADP, conformation 1
Sample
  • Sample: p97 in presence of ADP, conformation 1
  • Protein or peptide: Transitional endoplasmic reticulum ATPase
KeywordsAAA ATPase / p97
Function / homology
Function and homology information


RHOH GTPase cycle / HSF1 activation / Translesion Synthesis by POLH / Protein methylation / 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 / Translesion Synthesis by POLH / Protein methylation / 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 / positive regulation of ubiquitin-dependent protein catabolic process / 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 / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / aggresome assembly / NADH metabolic process / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / cellular response to misfolded protein / stress granule disassembly / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / retrograde protein transport, ER to cytosol / K48-linked polyubiquitin modification-dependent protein binding / regulation of synapse organization / positive regulation of ATP biosynthetic process / ATPase complex / ubiquitin-specific protease binding / MHC class I protein binding / polyubiquitin modification-dependent protein binding / autophagosome maturation / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / proteasomal protein catabolic process / interstrand cross-link repair / ATP metabolic process / negative regulation of smoothened signaling pathway / ERAD pathway / Neutrophil degranulation / proteasome complex / viral genome replication / lipid droplet / macroautophagy / ADP binding / positive regulation of protein-containing complex assembly / autophagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / 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 / ubiquitin-dependent protein catabolic process / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / protein domain specific binding / DNA repair / lipid binding / glutamatergic synapse / ubiquitin protein ligase binding / DNA damage response / 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 / cytosol / cytoplasm
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 / : / Aspartate decarboxylase-like domain superfamily ...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 / : / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / 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 speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsYeung HO / Forster A / Bebeacua C / Niwa H / Ewens C / McKeown C / Zhang X / Freemont PS
CitationJournal: 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
DepositionFeb 21, 2014-
Header (metadata) releaseFeb 26, 2014-
Map releaseFeb 26, 2014-
UpdateMar 19, 2014-
Current statusMar 19, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.96
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.96
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2590.jpg

Downloads & links

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Map

FileDownload / File: emd_2590.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of p97 in presence of ADP, conformation 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.53 Å/pix.
x 100 pix.
= 353. Å		3.53 Å/pix.
x 100 pix.
= 353. Å		3.53 Å/pix.
x 100 pix.
= 353. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.53 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.96 / Movie #1: 0.96
Minimum - Maximum-1.65855658 - 12.665450099999999
Average (Standard dev.)0.1039784 (±0.74347943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 353.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.533.533.53
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z353.000353.000353.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-207-207-206
NX/NY/NZ414414414
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-1.65912.6650.104

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Supplemental data

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Sample components

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Entire : p97 in presence of ADP, conformation 1

EntireName: p97 in presence of ADP, conformation 1
Components
  • Sample: p97 in presence of ADP, conformation 1
  • Protein or peptide: Transitional endoplasmic reticulum ATPase

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Supramolecule #1000: p97 in presence of ADP, conformation 1

SupramoleculeName: p97 in presence of ADP, conformation 1 / type: sample / ID: 1000 / Details: p97 E578Q mutant comprising residues 22-806 / Oligomeric state: homohexamer / Number unique components: 1
Molecular weightTheoretical: 550 KDa

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Macromolecule #1: Transitional endoplasmic reticulum ATPase

MacromoleculeName: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 1 / Name.synonym: VCP, P97 / Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: House mouse
Molecular weightTheoretical: 90 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pET28
SequenceUniProtKB: Transitional endoplasmic reticulum ATPase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.8 mg/mL
BufferpH: 8 / Details: 250 mM NaCl, 25 mM Tris, 2.5 mM MgCl2
GridDetails: carbon film on copper grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II / Method: Blot for two seconds before plunging.

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
DateMay 10, 2008
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm
Sample stageSpecimen holder model: GATAN HELIUM

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Image processing

Final reconstructionApplied 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: 30300
Final two d classificationNumber classes: 2

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Atomic model buiding 1

Initial modelPDB ID:

3cfc


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C
SoftwareName: VEDA
DetailsN, D1 and D2 domains fitted separately under imposition of sixfold symmetry
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient

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Atomic model buiding 2

Initial modelPDB ID:

1e32


Chain - Chain ID: A
SoftwareName: VEDA
DetailsN, D1 and D2 domains fitted separately under imposition of sixfold symmetry
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient

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