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- EMDB-2013: Electron microscopy negative staining map of the cross-linked p97... -

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Entry
Database: EMDB / ID: 2013
TitleElectron microscopy negative staining map of the cross-linked p97-Ufd1-Npl4 complex
KeywordsEM / p97 / Ufd1-Npl4 / asymmetric complex / ATPase
Samplep97-Ufd1-Npl4 cross-linked with glutaraldehyde
SourceMus musculus / mammal / House mouse / ハツカネズミ, はつかねずみ /
Rattus norvegicus / mammal / Norway rat / ドブネズミ, どぶねずみ /
Map dataSurface rendered p97-ATPase in complex with the adaptor Ufd1-Npl4
Methodsingle particle reconstruction, at 28 Å resolution
AuthorsBebeacua C / Forster A / McKeown C / Meyer HH / Zhang X / Freemont PS
CitationProc. Natl. Acad. Sci. U.S.A., 2012, 109, 1098-1103

Proc. Natl. Acad. Sci. U.S.A., 2012, 109, 1098-1103 StrPapers
Distinct conformations of the protein complex p97-Ufd1-Npl4 revealed by electron cryomicroscopy.
Cecilia Bebeacua / Andreas Förster / Ciarán McKeown / Hemmo H Meyer / Xiaodong Zhang / Paul S Freemont

DateDeposition: Dec 23, 2011 / Header (metadata) release: Jan 13, 2012 / Map release: Jan 13, 2012 / Last update: Dec 23, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.2
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_2013.map.gz (map file in CCP4 format, 8193 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
3.53 Å/pix.
= 451.84 Å
128 pix
3.53 Å/pix.
= 451.84 Å
128 pix
3.53 Å/pix.
= 451.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.53 Å
Density
Contour Level:4.2 (by author), 4.2 (movie #1):
Minimum - Maximum-1.68775 - 13.4836
Average (Standard dev.)0.115421 (0.819604)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin-64-64-64
Limit636363
Spacing128128128
CellA=B=C: 451.84 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-1.68813.4840.115

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Supplemental data

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Sample components

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Entire p97-Ufd1-Npl4 cross-linked with glutaraldehyde

EntireName: p97-Ufd1-Npl4 cross-linked with glutaraldehyde / Number of components: 3
Oligomeric State: One hexamer of p97 binds to one Ufd1-Npl4 dimer
MassTheoretical: 623 kDa / Experimental: 623 kDa

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Component #1: protein, p97

ProteinName: p97 / a.k.a: p97 / Number of Copies: 1 / Recombinant expression: Yes
SourceSpecies: Mus musculus / mammal / House mouse / ハツカネズミ, はつかねずみ /
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli
Strain: Rosetta
Source (natural)Location in cell: Cytoplasm

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Component #2: protein, Ufd1

ProteinName: Ufd1 / a.k.a: Ufd1 / Recombinant expression: Yes / Number of Copies: 1
SourceSpecies: Mus musculus / mammal / House mouse / ハツカネズミ, はつかねずみ /
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli
Strain: Rosetta
Source (natural)Location in cell: Cytoplasm

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Component #3: protein, Npl4

ProteinName: Npl4 / a.k.a: Npl4 / Number of Copies: 1 / Recombinant expression: Yes
SourceSpecies: Rattus norvegicus / mammal / Norway rat / ドブネズミ, どぶねずみ /
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli
Strain: Rosetta
Source (natural)Location in cell: Cytoplasm

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.05 mg/ml / Buffer solution: 25 mM HEPES, 500 mM KCl / pH: 8
Support film200 mesh copper grid
StainingGrids with adsorbed protein floated on 2% w/v uranyl acetate for 60 seconds.
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG / Date: Jul 1, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 50000 X (nominal), 50000 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3000 nm / Energy filter: FEI
Specimen HolderHolder: RT / Model: SIDE ENTRY, EUCENTRIC
CameraDetector: GENERIC CCD

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Image acquisition

Image acquisitionNumber of digital images: 1000

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 15000 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Back Projection / Software: IMAGIC / Resolution: 28 Å / Resolution method: FSC

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