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- EMDB-8086: Nuclear pore complex -

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Basic information

Entry
Database: EMDB / ID: EMD-8086
TitleNuclear pore complex
Map dataNone
Sample
  • Complex: Unmasked sub-unit of the inner ring of the human nuclear pore complex
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 25.2 Å
AuthorsMosalaganti S
CitationJournal: Science / Year: 2016
Title: Molecular architecture of the inner ring scaffold of the human nuclear pore complex.
Authors: Jan Kosinski / Shyamal Mosalaganti / Alexander von Appen / Roman Teimer / Amanda L DiGuilio / William Wan / Khanh Huy Bui / Wim J H Hagen / John A G Briggs / Joseph S Glavy / Ed Hurt / Martin Beck /
Abstract: Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these ...Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these nucleoporins assemble into the NPC scaffold imposes a formidable challenge. Recently, it has been shown how the Y complex, a prominent NPC module, forms the outer rings of the nuclear pore. However, the organization of the inner ring has remained unknown until now. We used molecular modeling combined with cross-linking mass spectrometry and cryo-electron tomography to obtain a composite structure of the inner ring. This architectural map explains the vast majority of the electron density of the scaffold. We conclude that despite obvious differences in morphology and composition, the higher-order structure of the inner and outer rings is unexpectedly similar.
History
DepositionFeb 22, 2016-
Header (metadata) releaseApr 27, 2016-
Map releaseApr 27, 2016-
UpdateApr 27, 2016-
Current statusApr 27, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 80.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 80.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8086.png

Downloads & links

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Map

FileDownload / File: emd_8086.map.gz / Format: CCP4 / Size: 11.4 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.)
6.7 Å/pix.
x 144 pix.
= 964.8 Å		6.7 Å/pix.
x 144 pix.
= 964.8 Å		6.7 Å/pix.
x 144 pix.
= 964.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 80.400000000000006 / Movie #1: 80.4
Minimum - Maximum-287.957699999999988 - 315.784240000000011
Average (Standard dev.)-12.224470999999999 (±26.960566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin349435
Dimensions144144144
Spacing144144144
CellA=B=C: 964.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.76.76.7
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z964.800964.800964.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS943435
NC/NR/NS144144144
D min/max/mean-287.958315.784-12.224

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Supplemental data

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Sample components

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Entire : Unmasked sub-unit of the inner ring of the human nuclear pore complex

EntireName: Unmasked sub-unit of the inner ring of the human nuclear pore complex
Components
  • Complex: Unmasked sub-unit of the inner ring of the human nuclear pore complex

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Supramolecule #1: Unmasked sub-unit of the inner ring of the human nuclear pore complex

SupramoleculeName: Unmasked sub-unit of the inner ring of the human nuclear pore complex
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / 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: 25.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 8400
ExtractionNumber tomograms: 101 / Number images used: 11112
Final angle assignmentType: OTHER

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