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- EMDB-8054: In situ sub-tomogram average of HeLa nuclear pore complex from a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-8054
TitleIn situ sub-tomogram average of HeLa nuclear pore complex from a single cell
Map dataNone
Sample
  • Complex: HeLa Nuclear Pore Complex
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 77.0 Å
AuthorsMahamid J / Pfeffer S / Schaffer M / Villa E / Danev R / Kuhn-Cuellar L / Foerster F / Hyman A / Plitzko J / Baumeister W
CitationJournal: Science / Year: 2016
Title: Visualizing the molecular sociology at the HeLa cell nuclear periphery.
Authors: Julia Mahamid / Stefan Pfeffer / Miroslava Schaffer / Elizabeth Villa / Radostin Danev / Luis Kuhn Cuellar / Friedrich Förster / Anthony A Hyman / Jürgen M Plitzko / Wolfgang Baumeister /
Abstract: The molecular organization of eukaryotic nuclear volumes remains largely unexplored. Here we combined recent developments in cryo-electron tomography (cryo-ET) to produce three-dimensional snapshots ...The molecular organization of eukaryotic nuclear volumes remains largely unexplored. Here we combined recent developments in cryo-electron tomography (cryo-ET) to produce three-dimensional snapshots of the HeLa cell nuclear periphery. Subtomogram averaging and classification of ribosomes revealed the native structure and organization of the cytoplasmic translation machinery. Analysis of a large dynamic structure-the nuclear pore complex-revealed variations detectable at the level of individual complexes. Cryo-ET was used to visualize previously elusive structures, such as nucleosome chains and the filaments of the nuclear lamina, in situ. Elucidation of the lamina structure provides insight into its contribution to metazoan nuclear stiffness.
History
DepositionJan 15, 2016-
Header (metadata) releaseMar 9, 2016-
Map releaseMar 9, 2016-
UpdateAug 26, 2020-
Current statusAug 26, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0242
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0242
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8054.png

Downloads & links

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Map

FileDownload / File: emd_8054.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
16.84 Å/pix.
x 128 pix.
= 2155.52 Å		16.84 Å/pix.
x 128 pix.
= 2155.52 Å		16.84 Å/pix.
x 128 pix.
= 2155.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 16.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0242 / Movie #1: 0.0242
Minimum - Maximum-0.099485785 - 0.152702
Average (Standard dev.)0.0000864243 (±0.019797916)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 2155.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z16.8416.8416.84
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z2155.5202155.5202155.520
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0990.1530.000

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Supplemental data

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Sample components

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Entire : HeLa Nuclear Pore Complex

EntireName: HeLa Nuclear Pore Complex
Components
  • Complex: HeLa Nuclear Pore Complex

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Supramolecule #1: HeLa Nuclear Pore Complex

SupramoleculeName: HeLa Nuclear Pore Complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Organelle: Nuclear envelope

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 0.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 77.0 Å / Resolution method: FSC 0.33 CUT-OFF / Number subtomograms used: 8
ExtractionNumber tomograms: 2 / Number images used: 8
Final angle assignmentType: NOT APPLICABLE

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