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- EMDB-2443: Electron microscopy of the human Nup107 subcomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-2443
TitleElectron microscopy of the human Nup107 subcomplex
Map dataReconstruction of the human Nup107 subcomplex
Sample
  • Sample: human Nup107 subcomplex
  • Protein or peptide: Human Nup107 subcomplex
Keywordsnuclear pore complex / Nup107 subcomplex / scaffold nucleoporins
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / Resolution: 34.0 Å
AuthorsBui KH / von Appen A / DiGuilio AL / Ori A / Sparks L / Mackmull MT / Bock T / Hagen W / Andres-Pons A / Glavy JS / Beck M
CitationJournal: Cell / Year: 2013
Title: Integrated structural analysis of the human nuclear pore complex scaffold.
Authors: Khanh Huy Bui / Alexander von Appen / Amanda L DiGuilio / Alessandro Ori / Lenore Sparks / Marie-Therese Mackmull / Thomas Bock / Wim Hagen / Amparo Andrés-Pons / Joseph S Glavy / Martin Beck /
Abstract: The nuclear pore complex (NPC) is a fundamental component of all eukaryotic cells that facilitates nucleocytoplasmic exchange of macromolecules. It is assembled from multiple copies of about 30 ...The nuclear pore complex (NPC) is a fundamental component of all eukaryotic cells that facilitates nucleocytoplasmic exchange of macromolecules. It is assembled from multiple copies of about 30 nucleoporins. Due to its size and complex composition, determining the structure of the NPC is an enormous challenge, and the overall architecture of the NPC scaffold remains elusive. In this study, we have used an integrated approach based on electron tomography, single-particle electron microscopy, and crosslinking mass spectrometry to determine the structure of a major scaffold motif of the human NPC, the Nup107 subcomplex, in both isolation and integrated into the NPC. We show that 32 copies of the Nup107 subcomplex assemble into two reticulated rings, one each at the cytoplasmic and nuclear face of the NPC. This arrangement may explain how changes of the diameter are realized that would accommodate transport of huge cargoes.
History
DepositionAug 22, 2013-
Header (metadata) releaseSep 25, 2013-
Map releaseDec 11, 2013-
UpdateDec 18, 2013-
Current statusDec 18, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 9.5
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2443.png

Downloads & links

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Map

FileDownload / File: emd_2443.map.gz / Format: CCP4 / Size: 2.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the human Nup107 subcomplex
Voxel sizeX=Y=Z: 5.84 Å
Density
Contour LevelBy AUTHOR: 9.5 / Movie #1: 9.5
Minimum - Maximum-9.28061295 - 23.715187069999999
Average (Standard dev.)-0.03333271 (±2.15004134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions848484
Spacing848484
CellA=B=C: 490.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.845.845.84
M x/y/z848484
origin x/y/z0.0000.0000.000
length x/y/z490.560490.560490.560
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS848484
D min/max/mean-9.28123.715-0.033

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Supplemental data

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Sample components

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Entire : human Nup107 subcomplex

EntireName: human Nup107 subcomplex
Components
  • Sample: human Nup107 subcomplex
  • Protein or peptide: Human Nup107 subcomplex

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Supramolecule #1000: human Nup107 subcomplex

SupramoleculeName: human Nup107 subcomplex / type: sample / ID: 1000
Details: The sample was affinity purified from HEK cells arrested by nocodazole.
Number unique components: 1
Molecular weightMethod: Gel filtration

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Macromolecule #1: Human Nup107 subcomplex

MacromoleculeName: Human Nup107 subcomplex / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Organelle: Nucleus / Location in cell: Nuclear pore complex

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Experimental details

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Structure determination

Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

GridDetails: 300 mesh Quantifoil Continous Carbon Support Copper Grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51369 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 34000
Sample stageSpecimen holder: Gatan 626, liquid nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
DateNov 26, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 300 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTF phase flip of each tomogram
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, SPIDER, TOM, AV3 / Number subtomograms used: 205
DetailsWe used a hybrid approach in which the primary data were acquired using a tomographic acquisition scheme, subtomograms were projected for two-dimensional classification and the resulting classes subjected to subtomogram averaging.

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