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- EMDB-32664: Cryo-EM map of the whole Saccharomyces cerevisiae nuclear pore complex -

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Basic information

Entry
Database: EMDB / ID: EMD-32664
TitleCryo-EM map of the whole Saccharomyces cerevisiae nuclear pore complex
Map data
Sample
  • Complex: Cryo-EM map of the whole Saccharomyces cerevisiae nuclear pore complex
Keywordsnuclear pore complex / Saccharomyces cerevisiae / cryo-EM / TRANSPORT PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.03 Å
AuthorsLi ZQ / Chen SJB / Zhao L / Sui SF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2022
Title: Near-atomic structure of the inner ring of the Saccharomyces cerevisiae nuclear pore complex.
Authors: Zongqiang Li / Shuaijiabin Chen / Liang Zhao / Guoqiang Huang / Xiong Pi / Shan Sun / Peiyi Wang / Sen-Fang Sui /
Abstract: Nuclear pore complexes (NPCs) mediate bidirectional nucleocytoplasmic transport of substances in eukaryotic cells. However, the accurate molecular arrangement of NPCs remains enigmatic owing to their ...Nuclear pore complexes (NPCs) mediate bidirectional nucleocytoplasmic transport of substances in eukaryotic cells. However, the accurate molecular arrangement of NPCs remains enigmatic owing to their huge size and highly dynamic nature. Here we determined the structure of the asymmetric unit of the inner ring (IR monomer) at 3.73 Å resolution by single-particle cryo-electron microscopy, and created an atomic model of the intact IR consisting of 192 molecules of 8 nucleoporins. In each IR monomer, the Z-shaped Nup188-Nup192 complex in the middle layer is sandwiched by two approximately parallel rhomboidal structures in the inner and outer layers, while Nup188, Nup192 and Nic96 link all subunits to constitute a relatively stable IR monomer. In contrast, the intact IR is assembled by loose and instable interactions between IR monomers. These structures, together with previously reported structural information of IR, reveal two distinct interaction modes between IR monomers and extensive flexible connections in IR assembly, providing a structural basis for the stability and malleability of IR.
History
DepositionJan 22, 2022-
Header (metadata) releaseApr 13, 2022-
Map releaseApr 13, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32664.png

Downloads & links

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Map

FileDownload / File: emd_32664.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.67 Å/pix.
x 512 pix.
= 1368.064 Å		2.67 Å/pix.
x 512 pix.
= 1368.064 Å		2.67 Å/pix.
x 512 pix.
= 1368.064 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.672 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.62225574 - 0.8702613
Average (Standard dev.)0.010529576 (±0.062001202)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 1368.064 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM map of the whole Saccharomyces cerevisiae nuclear pore complex

EntireName: Cryo-EM map of the whole Saccharomyces cerevisiae nuclear pore complex
Components
  • Complex: Cryo-EM map of the whole Saccharomyces cerevisiae nuclear pore complex

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Supramolecule #1: Cryo-EM map of the whole Saccharomyces cerevisiae nuclear pore complex

SupramoleculeName: Cryo-EM map of the whole Saccharomyces cerevisiae nuclear pore complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51220
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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