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- EMDB-1191: Conformational changes in the AAA ATPase p97-p47 adaptor complex. -

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Basic information

Entry
Database: EMDB / ID: EMD-1191
TitleConformational changes in the AAA ATPase p97-p47 adaptor complex.
Map dataAAA
Sample
  • Sample: Rat endogenous AAA ATPase p97 bound to p47, AMPPNP form
  • Protein or peptide: p97
  • Protein or peptide: p47
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 24.0 Å
AuthorsBeuron F / Dreveny I / Yuan X / Pye VE / McKeown C / Briggs LC / Cliff MJ / Kaneko Y / Wallis R / Isaacson RL ...Beuron F / Dreveny I / Yuan X / Pye VE / McKeown C / Briggs LC / Cliff MJ / Kaneko Y / Wallis R / Isaacson RL / Ladbury JE / Matthews SJ / Kondo H / Zhang X / Freemont PS
CitationJournal: EMBO J / Year: 2006
Title: Conformational changes in the AAA ATPase p97-p47 adaptor complex.
Authors: Fabienne Beuron / Ingrid Dreveny / Xuemei Yuan / Valerie E Pye / Ciaran McKeown / Louise C Briggs / Matthew J Cliff / Yayoi Kaneko / Russell Wallis / Rivka L Isaacson / John E Ladbury / ...Authors: Fabienne Beuron / Ingrid Dreveny / Xuemei Yuan / Valerie E Pye / Ciaran McKeown / Louise C Briggs / Matthew J Cliff / Yayoi Kaneko / Russell Wallis / Rivka L Isaacson / John E Ladbury / Steve J Matthews / Hisao Kondo / Xiaodong Zhang / Paul S Freemont /
Abstract: The AAA+ATPase p97/VCP, helped by adaptor proteins, exerts its essential role in cellular events such as endoplasmic reticulum-associated protein degradation or the reassembly of Golgi, ER and the ...The AAA+ATPase p97/VCP, helped by adaptor proteins, exerts its essential role in cellular events such as endoplasmic reticulum-associated protein degradation or the reassembly of Golgi, ER and the nuclear envelope after mitosis. Here, we report the three-dimensional cryo-electron microscopy structures at approximately 20 Angstroms resolution in two nucleotide states of the endogenous hexameric p97 in complex with a recombinant p47 trimer, one of the major p97 adaptor proteins involved in membrane fusion. Depending on the nucleotide state, we observe the p47 trimer to be in two distinct arrangements on top of the p97 hexamer. By combining the EM data with NMR and other biophysical measurements, we propose a model of ATP-dependent p97(N) domain motions that lead to a rearrangement of p47 domains, which could result in the disassembly of target protein complexes.
History
DepositionFeb 22, 2006-
Header (metadata) releaseFeb 22, 2006-
Map releaseMay 9, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.21
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.21
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1191.gif

Downloads & links

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Map

FileDownload / File: emd_1191.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAAA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.6 Å/pix.
x 150 pix.
= 390. Å		2.6 Å/pix.
x 150 pix.
= 390. Å		2.6 Å/pix.
x 150 pix.
= 390. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.6 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.356 / Movie #1: 0.21
Minimum - Maximum-2.85389 - 3.53379
Average (Standard dev.)0.00159886 (±0.177)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-75-75-75
Dimensions150150150
Spacing150150150
CellA=B=C: 390 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.62.62.6
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z390.000390.000390.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-96-96
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS-75-75-75
NC/NR/NS150150150
D min/max/mean-2.8543.5340.002

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Supplemental data

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Sample components

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Entire : Rat endogenous AAA ATPase p97 bound to p47, AMPPNP form

EntireName: Rat endogenous AAA ATPase p97 bound to p47, AMPPNP form
Components
  • Sample: Rat endogenous AAA ATPase p97 bound to p47, AMPPNP form
  • Protein or peptide: p97
  • Protein or peptide: p47

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Supramolecule #1000: Rat endogenous AAA ATPase p97 bound to p47, AMPPNP form

SupramoleculeName: Rat endogenous AAA ATPase p97 bound to p47, AMPPNP form
type: sample / ID: 1000 / Oligomeric state: p97 hexamer bound to p47 trimer / Number unique components: 2
Molecular weightExperimental: 650 KDa / Method: STEM

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Macromolecule #1: p97

MacromoleculeName: p97 / type: protein_or_peptide / ID: 1 / Name.synonym: VCP / Number of copies: 6 / Oligomeric state: hexamer / Recombinant expression: No
Source (natural)Organism: Rattus norvegicus (Norway rat) / Tissue: liver / Location in cell: cytoplasmic
Molecular weightTheoretical: 89 MDa

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Macromolecule #2: p47

MacromoleculeName: p47 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 41 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pQE-30

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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

Concentration0.7 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris-HCl, 150 mM KCl, 1 mM DTT, pH 7.4
GridDetails: lacey carbon film
VitrificationCryogen name: ETHANE / Instrument: LEICA KF80 / Details: Vitrification instrument: Reichert KF 80 plunger / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
DateJun 6, 2002
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.35 µm / Number real images: 7 / Average electron dose: 15 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 38000
Sample stageSpecimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic / Number images used: 5400
Final two d classificationNumber classes: 95

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Atomic model buiding 1

RefinementSpace: RECIPROCAL

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