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- EMDB-1097: Nuclear pore complex structure and dynamics revealed by cryoelect... -

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Basic information

Entry
Database: EMDB / ID: EMD-1097
TitleNuclear pore complex structure and dynamics revealed by cryoelectron tomography.
Map data3D structure of the Dictyostelium nuclear pore complex obtained by Cryoelectron Tomography
Sample
  • Sample: nuclear pore complex
  • Protein or peptide: nuclear pore complex
Biological speciesDictyostelium discoideum (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 85.0 Å
AuthorsBeck M / Forster F / Ecke M / Plitzko JM / Melchior F / Gerisch G / Baumeister W / Medalia O
CitationJournal: Science / Year: 2004
Title: Nuclear pore complex structure and dynamics revealed by cryoelectron tomography.
Authors: Martin Beck / Friedrich Förster / Mary Ecke / Jürgen M Plitzko / Frauke Melchior / Günther Gerisch / Wolfgang Baumeister / Ohad Medalia /
Abstract: Nuclear pore complexes (NPCs) are gateways for nucleocytoplasmic exchange. To analyze their structure in a close-to-life state, we studied transport-active, intact nuclei from Dictyostelium ...Nuclear pore complexes (NPCs) are gateways for nucleocytoplasmic exchange. To analyze their structure in a close-to-life state, we studied transport-active, intact nuclei from Dictyostelium discoideum by means of cryoelectron tomography. Subvolumes of the tomograms containing individual NPCs were extracted in silico and subjected to three-dimensional classification and averaging, whereby distinct structural states were observed. The central plug/transporter (CP/T) was variable in volume and could occupy different positions along the nucleocytoplasmic axis, which supports the notion that it essentially represents cargo in transit. Changes in the position of the CP/T were accompanied by structural rearrangements in the NPC scaffold.
History
DepositionSep 13, 2004-
Header (metadata) releaseSep 23, 2004-
Map releaseSep 23, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.404
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.404
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1097.gif

Downloads & links

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Map

FileDownload / File: emd_1097.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D structure of the Dictyostelium nuclear pore complex obtained by Cryoelectron Tomography
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
16.4 Å/pix.
x 128 pix.
= 2099.2 Å		16.4 Å/pix.
x 128 pix.
= 2099.2 Å		16.4 Å/pix.
x 128 pix.
= 2099.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 16.4 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1.22 / Movie #1: 1.404
Minimum - Maximum-3.05764 - 3.81137
Average (Standard dev.)0.0933206 (±0.55606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 2099.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z16.416.416.4
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z2099.2002099.2002099.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-56-288
NX/NY/NZ192112576
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-3.0583.8110.093

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Supplemental data

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Sample components

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Entire : nuclear pore complex

EntireName: nuclear pore complex
Components
  • Sample: nuclear pore complex
  • Protein or peptide: nuclear pore complex

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Supramolecule #1000: nuclear pore complex

SupramoleculeName: nuclear pore complex / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: nuclear pore complex

MacromoleculeName: nuclear pore complex / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Dictyostelium discoideum (eukaryote) / Strain: AX2 / Organelle: Nucleus / Location in cell: Nucleus

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferDetails: 50 mM Tris pH 7.6, 25 mM KCl, 5mM MgCl2, 50 mM sucrose
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Rudolf Gatz plunger

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
TemperatureAverage: 90 K
Specialist opticsEnergy filter - Name: GIF2000 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Image recordingCategory: CCD / Film or detector model: GATAN MULTISCAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 17500
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Max angle: 63 °

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Image processing

DetailsAverage number of projections used in the 3D reconstructions: 267.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 85.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: TOM / Details: 3D reconstruction by averaging of subtomograms

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