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- EMDB-4355: Chlamydomonas reinhardtii nuclear pore complex -

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Basic information

Database: EMDB / ID: 4355
TitleChlamydomonas reinhardtii nuclear pore complex
Map dataElectron density map of the Chlamydomonas reinhardtii Nuclear pore complex
SampleFocus Ion Beam milled Chlamydomonas cells:
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 31, 2018 / Header (metadata) release: May 23, 2018 / Map release: Jul 4, 2018 / Last update: Jul 4, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_4355.map.gz (map file in CCP4 format, 70305 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
260 pix
6.84 Å/pix.
= 1778.4 Å
260 pix
6.84 Å/pix.
= 1778.4 Å
260 pix
6.84 Å/pix.
= 1778.4 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.84 Å
Contour Level:1.0 (by author), 1 (movie #1):
Minimum - Maximum-3.84082 - 6.5159717
Average (Standard dev.)-0.0044762474 (0.35131323)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 1778.4 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/z260260260
origin x/y/z0.0000.0000.000
length x/y/z1778.4001778.4001778.400
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-3.8416.516-0.004

Supplemental data

Sample components

Entire Focus Ion Beam milled Chlamydomonas cells

EntireName: Focus Ion Beam milled Chlamydomonas cells / Number of components: 1

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)

Experimental details

Sample preparation

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

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)

Image processing

ProcessingMethod: subtomogram averaging / Number of subtomograms: 624
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF

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