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- EMDB-7479: Cdc48-Npl4 complex in the presence of ADP -

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Basic information

Entry
Database: EMDB / ID: 7479
TitleCdc48-Npl4 complex in the presence of ADP
Map dataCdc48-Npl4 complex in the presence of ATP-gamma-S
SampleCdc48-Npl4/Ufd1 complex:
Cdc48 / Npl4
SourceChaetomium thermophilum (fungus)
Methodsingle particle reconstruction / cryo EM / 6.7 Å resolution
AuthorsKim KH / Bodnar NO
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4.
Authors: Nicholas O Bodnar / Kelly H Kim / Zhejian Ji / Thomas E Wales / Vladimir Svetlov / Evgeny Nudler / John R Engen / Thomas Walz / Tom A Rapoport
DateDeposition: Feb 23, 2018 / Header (metadata) release: Mar 21, 2018 / Map release: Jul 4, 2018 / Last update: Dec 5, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7479.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.021079905 - 0.07750744
Average (Standard dev.)0.0006778931 (0.0042213453)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 332.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0210.0780.001

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Supplemental data

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Sample components

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Entire Cdc48-Npl4/Ufd1 complex

EntireName: Cdc48-Npl4/Ufd1 complex / Number of components: 3

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Component #1: cellular-component, Cdc48-Npl4/Ufd1 complex

Cellular-componentName: Cdc48-Npl4/Ufd1 complex / Recombinant expression: No
SourceSpecies: Chaetomium thermophilum (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Cdc48

ProteinName: Cdc48 / Recombinant expression: No
SourceSpecies: Chaetomium thermophilum (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Npl4

ProteinName: Npl4 / Recombinant expression: No
SourceSpecies: Chaetomium thermophilum (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/ml / pH: 7.5
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200.0 - 2800.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3279

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 52178
3D reconstructionSoftware: RELION / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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