+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8086 | |||||||||
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Title | Nuclear pore complex | |||||||||
Map data | None | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 25.2 Å | |||||||||
Authors | Mosalaganti S | |||||||||
Citation | Journal: 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 |
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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_8086.map.gz | 10.5 MB | EMDB map data format | |
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Header (meta data) | emd-8086-v30.xml emd-8086.xml | 7.6 KB 7.6 KB | Display Display | EMDB header |
Images | emd_8086.png | 125.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8086 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8086 | HTTPS FTP |
-Validation report
Summary document | emd_8086_validation.pdf.gz | 78 KB | Display | EMDB validaton report |
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Full document | emd_8086_full_validation.pdf.gz | 77.1 KB | Display | |
Data in XML | emd_8086_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8086 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8086 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8086.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.7 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 : Unmasked sub-unit of the inner ring of the human nuclear pore complex
Entire | Name: Unmasked sub-unit of the inner ring of the human nuclear pore complex |
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Components |
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-Supramolecule #1: Unmasked sub-unit of the inner ring of the human nuclear pore complex
Supramolecule | Name: Unmasked sub-unit of the inner ring of the human nuclear pore complex type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-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: 3.0 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: 25.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 8400 |
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Extraction | Number tomograms: 101 / Number images used: 11112 |
Final angle assignment | Type: OTHER |