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- EMDB-2016: CryoEM map of the p97-Ufd1-Npl4 complex in the single-binding-sit... -

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Basic information

Entry
Database: EMDB / ID: EMD-2016
TitleCryoEM map of the p97-Ufd1-Npl4 complex in the single-binding-site conformation
Map datap97-Ufd1-Npl4 complex in the single-binding-site conformation
Sample
  • Sample: p97-Ufd1-Npl4
  • Protein or peptide: p97
  • Protein or peptide: Ufd1
  • Protein or peptide: Npl4
Keywordsp97 / Ufd1-Npl4 / asymmetric complex / ATPase
Biological speciesMus musculus (house mouse) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsBebeacua C / Forster A / McKeown C / Meyer HH / Zhang X / Freemont PS
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Distinct conformations of the protein complex p97-Ufd1-Npl4 revealed by electron cryomicroscopy.
Authors: Cecilia Bebeacua / Andreas Förster / Ciarán McKeown / Hemmo H Meyer / Xiaodong Zhang / Paul S Freemont /
Abstract: p97 is a key regulator of numerous cellular pathways and associates with ubiquitin-binding adaptors to remodel ubiquitin-modified substrate proteins. How adaptor binding to p97 is coordinated and how ...p97 is a key regulator of numerous cellular pathways and associates with ubiquitin-binding adaptors to remodel ubiquitin-modified substrate proteins. How adaptor binding to p97 is coordinated and how adaptors contribute to substrate remodeling is unclear. Here we present the 3D electron cryomicroscopy reconstructions of the major Ufd1-Npl4 adaptor in complex with p97. Our reconstructions show that p97-Ufd1-Npl4 is highly dynamic and that Ufd1-Npl4 assumes distinct positions relative to the p97 ring upon addition of nucleotide. Our results suggest a model for substrate remodeling by p97 and also explains how p97-Ufd1-Npl4 could form other complexes in a hierarchical model of p97-cofactor assembly.
History
DepositionDec 23, 2011-
Header (metadata) releaseJan 13, 2012-
Map releaseJan 13, 2012-
UpdateJun 10, 2015-
Current statusJun 10, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd2016fig.png

Downloads & links

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Map

FileDownload / File: emd_2016.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationp97-Ufd1-Npl4 complex in the single-binding-site conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.53 Å/pix.
x 128 pix.
= 451.84 Å		3.53 Å/pix.
x 128 pix.
= 451.84 Å		3.53 Å/pix.
x 128 pix.
= 451.84 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: 0.3 / Movie #1: 0.3
Minimum - Maximum-1.91861 - 18.5168
Average (Standard dev.)0.0814002 (±0.747048)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 451.84 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.533.533.53
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z451.840451.840451.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-1.91918.5170.081

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Supplemental data

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Sample components

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Entire : p97-Ufd1-Npl4

EntireName: p97-Ufd1-Npl4
Components
  • Sample: p97-Ufd1-Npl4
  • Protein or peptide: p97
  • Protein or peptide: Ufd1
  • Protein or peptide: Npl4

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Supramolecule #1000: p97-Ufd1-Npl4

SupramoleculeName: p97-Ufd1-Npl4 / type: sample / ID: 1000
Oligomeric state: One hexamer of p97 binds to one Ufd1-Npl4 dimer
Number unique components: 3
Molecular weightExperimental: 623 KDa / Theoretical: 623 KDa

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Macromolecule #1: p97

MacromoleculeName: p97 / type: protein_or_peptide / ID: 1 / Name.synonym: p97 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: House mouse / Location in cell: Cytoplasm
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta

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Macromolecule #2: Ufd1

MacromoleculeName: Ufd1 / type: protein_or_peptide / ID: 2 / Name.synonym: Ufd1 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: House mouse / Location in cell: Cytoplasm
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta

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Macromolecule #3: Npl4

MacromoleculeName: Npl4 / type: protein_or_peptide / ID: 3 / Name.synonym: Npl4 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: Norway rat / Location in cell: Cytoplasm
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta

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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

Concentration0.5 mg/mL
BufferpH: 8 / Details: 150 mM KCL, 25 mL Tris, 2.5 mM MgCl2
GridDetails: 200 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Specialist opticsEnergy filter - Name: FEI
DateJul 1, 2009
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Number real images: 100 / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: IMAGIC / Number images used: 5000

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Atomic model buiding 1

Initial modelPDB ID:

1r7r

SoftwareName: Chimera
DetailsProtocol: Rigid Body. The protomers were fitted individually and the N-domains fitted by manual docking and refined automatically
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross Correlation

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