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- EMDB-3820: Electron tomographic slices of the nuclear envelope of HeLa cell ... -

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Basic information

Database: EMDB / ID: 3820
TitleElectron tomographic slices of the nuclear envelope of HeLa cell in interphase
Map data
SampleHeLa cell:
SourceHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsOtsuka S / Ellenberg J
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Postmitotic nuclear pore assembly proceeds by radial dilation of small membrane openings.
Authors: Shotaro Otsuka / Anna M Steyer / Martin Schorb / Jean-Karim Hériché / M Julius Hossain / Suruchi Sethi / Moritz Kueblbeck / Yannick Schwab / Martin Beck / Jan Ellenberg
DateDeposition: Jul 20, 2017 / Header (metadata) release: Aug 23, 2017 / Map release: Nov 29, 2017 / Last update: Jan 24, 2018

Structure visualization

  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Simplified surface model
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Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_3820.map.gz (map file in CCP4 format, 1946156 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
326 pix
7.5 Å/pix.
= 2445. Å
4096 pix
7.5 Å/pix.
= 30720. Å
4096 pix
7.5 Å/pix.
= 30720. Å


Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.5 Å
Contour Level:255 (by author)
Minimum - Maximum-4205 - 1647
Average (Standard dev.)173.76695 (219.1015)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 30720 Å / B: 30720 Å / C: 2445 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z7.57.57.5
M x/y/z40964096326
origin x/y/z0.0000.0000.000
length x/y/z30720.00030720.0002445.000
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS00150
D min/max/mean-4205.0001647.000173.767

Supplemental data

Sample components

Entire HeLa cell

EntireName: HeLa cell
Details: Cells were high-pressure frozen and freeze-substituted into Lowicryl resin.
Number of components: 1

Component #1: cellular-component, HeLa cell

Cellular-componentName: HeLa cell
Details: Cells were high-pressure frozen and freeze-substituted into Lowicryl resin.
Recombinant expression: No
SourceSpecies: Homo sapiens (human) / Strain: HeLa

Experimental details

Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionBuffer solution: CO2-independent medium without phenol red (Invitrogen), containing 20% FCS, 20% Ficoll PM400 2 mM l-glutamine, and 100 ug/ml penicillin and streptomycin
pH: 7.4
VitrificationCryogen name: NITROGEN

Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 200 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 15500 X (nominal) / Cs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - nm
Specimen HolderModel: OTHER / Tilt Angle: -60 - 60 deg.
CameraDetector: FEI EAGLE (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 121
Raw dataEMPIAR-10116 (Title: Raw 2d tomographic tilt series of a dividing cell / Data size: 245.4
Data #1: Raw 2D tilt series for all the electron tomograms [tilt series])

Image processing

ProcessingMethod: electron tomography / Tilt angle increment: 1 deg. / Number of sections: 121
3D reconstructionAlgorithm: BACK PROJECTION / Software: IMOD
Details: Dual axis tilt series were aligned using gold fiducial markers

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