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- EMDB-4332: Segment of the cytoplasmic ring of the Chlamydomonas reinhardtii ... -

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Basic information

Entry
Database: EMDB / ID: EMD-4332
TitleSegment of the cytoplasmic ring of the Chlamydomonas reinhardtii nuclear pore complex
Map dataSegment of the cytoplasmic ring of the Chlamydomonas reinhardtii nuclear pore complex
Sample
  • Organelle or cellular component: Focus Ion Beam milled Chlamydomonas cells
    • Other: Nuclear pore complex
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 30.0 Å
AuthorsMosalaganti S / Albert S / Engel BD / Beck M
CitationJournal: Nat Commun / Year: 2018
Title: In situ architecture of the algal nuclear pore complex.
Authors: Shyamal Mosalaganti / Jan Kosinski / Sahradha Albert / Miroslava Schaffer / Daniela Strenkert / Patrice A Salomé / Sabeeha S Merchant / Jürgen M Plitzko / Wolfgang Baumeister / Benjamin D ...Authors: Shyamal Mosalaganti / Jan Kosinski / Sahradha Albert / Miroslava Schaffer / Daniela Strenkert / Patrice A Salomé / Sabeeha S Merchant / Jürgen M Plitzko / Wolfgang Baumeister / Benjamin D Engel / Martin Beck /
Abstract: Nuclear pore complexes (NPCs) span the nuclear envelope and mediate nucleocytoplasmic exchange. They are a hallmark of eukaryotes and deeply rooted in the evolutionary origin of cellular ...Nuclear pore complexes (NPCs) span the nuclear envelope and mediate nucleocytoplasmic exchange. They are a hallmark of eukaryotes and deeply rooted in the evolutionary origin of cellular compartmentalization. NPCs have an elaborate architecture that has been well studied in vertebrates. Whether this architecture is unique or varies significantly in other eukaryotic kingdoms remains unknown, predominantly due to missing in situ structural data. Here, we report the architecture of the algal NPC from the early branching eukaryote Chlamydomonas reinhardtii and compare it to the human NPC. We find that the inner ring of the Chlamydomonas NPC has an unexpectedly large diameter, and the outer rings exhibit an asymmetric oligomeric state that has not been observed or predicted previously. Our study provides evidence that the NPC is subject to substantial structural variation between species. The divergent and conserved features of NPC architecture provide insights into the evolution of the nucleocytoplasmic transport machinery.
History
DepositionMar 12, 2018-
Header (metadata) releaseMay 16, 2018-
Map releaseJul 4, 2018-
UpdateJul 4, 2018-
Current statusJul 4, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4332.png

Downloads & links

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Map

FileDownload / File: emd_4332.map.gz / Format: CCP4 / Size: 8.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSegment of the cytoplasmic ring of the Chlamydomonas reinhardtii nuclear pore complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.84 Å/pix.
x 130 pix.
= 889.2 Å		6.84 Å/pix.
x 130 pix.
= 889.2 Å		6.84 Å/pix.
x 130 pix.
= 889.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.05 / Movie #1: 2.05
Minimum - Maximum-11.725752 - 18.268650000000001
Average (Standard dev.)-0.000000000954303 (±1.0930823)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions130130130
Spacing130130130
CellA=B=C: 889.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.846.846.84
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z889.200889.200889.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
D min/max/mean-11.72618.269-0.000

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Supplemental data

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Sample components

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Entire : Focus Ion Beam milled Chlamydomonas cells

EntireName: Focus Ion Beam milled Chlamydomonas cells
Components
  • Organelle or cellular component: Focus Ion Beam milled Chlamydomonas cells
    • Other: Nuclear pore complex

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Supramolecule #1: Focus Ion Beam milled Chlamydomonas cells

SupramoleculeName: Focus Ion Beam milled Chlamydomonas cells / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Macromolecule #1: Nuclear pore complex

MacromoleculeName: Nuclear pore complex / type: other / ID: 1 / Classification: other
SequenceString:
None

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 2.5 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: 30.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 624
ExtractionNumber tomograms: 76 / Number images used: 78
Final angle assignmentType: NOT APPLICABLE

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