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- EMDB-4332: Segment of the cytoplasmic ring of the Chlamydomonas reinhardtii ... -

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Basic information

Entry
Database: EMDB / ID: 4332
TitleSegment of the cytoplasmic ring of the Chlamydomonas reinhardtii nuclear pore complex
Map dataSegment of the cytoplasmic ring of the Chlamydomonas reinhardtii nuclear pore complex
SampleFocus Ion Beam milled Chlamydomonas cells:
nucleic-acidNucleic acid
SourceChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / 30 Å resolution
AuthorsMosalaganti S / Albert S / Engel BD / Beck M
CitationJournal: Nat Commun / Year: 2018
Title: In situ architecture of the algal nuclear pore complex.
Authors: Shyamal Mosalaganti / Jan Kosinski / Sahradha Albert / Miroslava Schaffer / Daniela Strenkert / Patrice A Salomé / Sabeeha S Merchant / Jürgen M Plitzko / Wolfgang Baumeister / Benjamin D Engel / Martin Beck
DateDeposition: Mar 12, 2018 / Header (metadata) release: May 16, 2018 / Map release: Jul 4, 2018 / Last update: Jul 4, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4332.map.gz (map file in CCP4 format, 8789 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
130 pix
6.84 Å/pix.
= 889.2 Å
130 pix
6.84 Å/pix.
= 889.2 Å
130 pix
6.84 Å/pix.
= 889.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.84 Å
Density
Contour Level:2.05 (by author), 2.05 (movie #1):
Minimum - Maximum-11.725752 - 18.268650000000001
Average (Standard dev.)-0.000000000954303 (1.0930823)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions130130130
Origin0.0.0.
Limit129.129.129.
Spacing130130130
CellA=B=C: 889.2 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.846.846.84
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z889.200889.200889.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
D min/max/mean-11.72618.269-0.000

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Supplemental data

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Sample components

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Entire Focus Ion Beam milled Chlamydomonas cells

EntireName: Focus Ion Beam milled Chlamydomonas cells / Number of components: 2

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Component #1: cellular-component, Focus Ion Beam milled Chlamydomonas cells

Cellular-componentName: Focus Ion Beam milled Chlamydomonas cells / Recombinant expression: No
SourceSpecies: Chlamydomonas reinhardtii (plant)

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Component #2: nucleic-acid, Nuclear pore complex

Nucleic-acidName: Nuclear pore complexNuclear pore / Class: OTHER / Structure: OTHER / Synthetic: No
Sequence:
None

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Experimental details

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Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER

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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: 2.5 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 624
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF

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