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Yorodumi- EMDB-4332: Segment of the cytoplasmic ring of the Chlamydomonas reinhardtii ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4332 | |||||||||
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Title | Segment of the cytoplasmic ring of the Chlamydomonas reinhardtii nuclear pore complex | |||||||||
Map data | Segment of the cytoplasmic ring of the Chlamydomonas reinhardtii nuclear pore complex | |||||||||
Sample |
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Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 30.0 Å | |||||||||
Authors | Mosalaganti S / Albert S / Engel BD / Beck M | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4332.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-4332-v30.xml emd-4332.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | emd_4332.png | 33.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4332 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4332 | HTTPS FTP |
-Validation report
Summary document | emd_4332_validation.pdf.gz | 215.8 KB | Display | EMDB validaton report |
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Full document | emd_4332_full_validation.pdf.gz | 215 KB | Display | |
Data in XML | emd_4332_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4332 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4332 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4332.map.gz / Format: CCP4 / Size: 8.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Segment of the cytoplasmic ring of the Chlamydomonas reinhardtii nuclear pore complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Focus Ion Beam milled Chlamydomonas cells
Entire | Name: Focus Ion Beam milled Chlamydomonas cells |
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Components |
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-Supramolecule #1: Focus Ion Beam milled Chlamydomonas cells
Supramolecule | Name: Focus Ion Beam milled Chlamydomonas cells / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
-Macromolecule #1: Nuclear pore complex
Macromolecule | Name: Nuclear pore complex / type: other / ID: 1 / Classification: other |
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Sequence | String: None |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 2.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 624 |
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Extraction | Number tomograms: 76 / Number images used: 78 |
Final angle assignment | Type: NOT APPLICABLE |