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- EMDB-3939: Local refinement of the extra density that tethers 26S proteasome... -

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Entry
Database: EMDB / ID: 3939
TitleLocal refinement of the extra density that tethers 26S proteasomes to the NPC basket
SampleLocal refinement of the extra density that tethers 26S proteasomes to the NPC basket
SourceChlamydomonas reinhardtii / plant
Map data
Methodsubtomogram averaging, at 36.48 Å resolution
AuthorsAlbert S / Schaffer M / Beck F / Mosalaganti S / Asano S / Thomas HF / Plitzko J / Beck M / Baumeister W / Engel BD
CitationTo be published

To be published Search PubMed
Proteasomes tether to two distinct sites at the nuclear pore complex
Albert S / Schaffer M / Beck F / Mosalaganti S / Asano S / Thomas HF / Plitzko J / Beck M / Baumeister W / Engel BD

DateDeposition: Oct 17, 2017 / Header (metadata) release: Oct 25, 2017 / Map release: Oct 25, 2017 / Last update: Oct 25, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_3939.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
3.42 Å/pix.
= 684. Å
200 pix
3.42 Å/pix.
= 684. Å
200 pix
3.42 Å/pix.
= 684. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.42 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.11974485 - 0.15491162
Average (Standard dev.)0.00010926692 (0.007977651)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 684 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.423.423.42
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z684.000684.000684.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1200.1550.000

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Supplemental data

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Sample components

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Entire Local refinement of the extra density that tethers 26S proteasome...

EntireName: Local refinement of the extra density that tethers 26S proteasomes to the NPC basket
Details: Fusion structure of two in situ subtomogram averages: the 26S double-capped proteasome (EMDB-3932) and a local refinement of the extra density tethering the proteasome to the NPC basket (EMDB-3937). Proteasomes were imaged within the native Chlamydomonas cell. Cells were thinned by focused ion beam milling.
Number of components: 1
MassTheoretical: 2 MDa

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Component #1: protein, Local refinement of the extra density that tethers 26S p...

ProteinName: Local refinement of the extra density that tethers 26S proteasomes to the NPC basket
Details: Fusion structure of two in situ subtomogram averages: the 26S double-capped proteasome (EMDB-3932) and a local refinement of the extra density tethering the proteasome to the NPC basket (EMDB-3937). Proteasomes were imaged within the native Chlamydomonas cell. Cells were thinned by focused ion beam milling.
Recombinant expression: No
MassTheoretical: 2 MDa
SourceSpecies: Chlamydomonas reinhardtii / plant / Strain: mat3-4
Source (natural)Organelle: nucleus / Location in cell: nuclear pore complex basket

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Experimental details

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Sample preparation

Specimen statecell
Sample solutionpH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 293 K / Humidity: 90 %
Details: Blotted for 10 seconds with 10 blot force before plunging.

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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: 1.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 42000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 4000 - 6000 nm / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -60 - 60 deg.
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionDetails: Images were collected in movie mode at 12 frames per second

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric)
3D reconstructionResolution: 36.48 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Fusion of a 26S double-capped proteasome subtomogram average (EMDB-3932) with locally refined extra density from the basket-tethered 26S proteasome subtomogram average (EMDB-3937)

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