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- EMDB-3009: Cytoplasmic ring of the actinomycin D treated X. laevis nuclear p... -

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Basic information

Entry
Database: EMDB / ID: EMD-3009
TitleCytoplasmic ring of the actinomycin D treated X. laevis nuclear pore complex.
Map dataRecommended UCSF Chimera hide dust setting: size 43.0
Sample
  • Sample: X. laevis nuclear pore complex
  • Protein or peptide: Nuclear pore complex
KeywordsX. laevis / Nuclear pore complex / Cytoplasmic ring / Actinomycin D
Biological speciesXenopus laevis (African clawed frog)
Methodsubtomogram averaging / cryo EM
AuthorsEibauer M / Pellanda M / Turgay Y / Dubrovsky A / Wild A / Medalia O
CitationJournal: Nat Commun / Year: 2015
Title: Structure and gating of the nuclear pore complex.
Authors: Matthias Eibauer / Mauro Pellanda / Yagmur Turgay / Anna Dubrovsky / Annik Wild / Ohad Medalia /
Abstract: Nuclear pore complexes (NPCs) perforate the nuclear envelope and allow the exchange of macromolecules between the nucleus and the cytoplasm. To acquire a deeper understanding of this transport ...Nuclear pore complexes (NPCs) perforate the nuclear envelope and allow the exchange of macromolecules between the nucleus and the cytoplasm. To acquire a deeper understanding of this transport mechanism, we analyse the structure of the NPC scaffold and permeability barrier, by reconstructing the Xenopus laevis oocyte NPC from native nuclear envelopes up to 20 Å resolution by cryo-electron tomography in conjunction with subtomogram averaging. In addition to resolving individual protein domains of the NPC constituents, we propose a model for the architecture of the molecular gate at its central channel. Furthermore, we compare and contrast this native NPC structure to one that exhibits reduced transport activity and unveil the spatial properties of the NPC gate.
History
DepositionMay 13, 2015-
Header (metadata) releaseJun 17, 2015-
Map releaseJul 1, 2015-
UpdateJul 15, 2015-
Current statusJul 15, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3009.tif

Downloads & links

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Map

FileDownload / File: emd_3009.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRecommended UCSF Chimera hide dust setting: size 43.0
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.6 Å/pix.
x 256 pix.
= 1689.6 Å		6.6 Å/pix.
x 256 pix.
= 1689.6 Å		6.6 Å/pix.
x 256 pix.
= 1689.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.9 / Movie #1: 4.9
Minimum - Maximum-15.74595261 - 51.05454254
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 1689.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.66.66.6
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z1689.6001689.6001689.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-15.74651.055-0.000

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Supplemental data

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Sample components

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Entire : X. laevis nuclear pore complex

EntireName: X. laevis nuclear pore complex
Components
  • Sample: X. laevis nuclear pore complex
  • Protein or peptide: Nuclear pore complex

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Supramolecule #1000: X. laevis nuclear pore complex

SupramoleculeName: X. laevis nuclear pore complex / type: sample / ID: 1000 / Details: The sample was treated with Actinomycin D. / Number unique components: 1

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Macromolecule #1: Nuclear pore complex

MacromoleculeName: Nuclear pore complex / type: protein_or_peptide / ID: 1 / Name.synonym: NPC / Recombinant expression: No
Source (natural)Organism: Xenopus laevis (African clawed frog) / synonym: African clawed frog / Cell: Oocyte / Organelle: Nucleus / Location in cell: Nuclear envelope

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateJun 10, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.5 µm / Nominal defocus min: 5.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution method: OTHER / Software - Name: TOM / Details: Protomer averaging, subprotomer averaging / Number subtomograms used: 3409
CTF correctionDetails: Whole micrograph

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