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Yorodumi- EMDB-8087: Molecular architecture of the inner ring scaffold of the human nu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8087 | |||||||||
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Title | Molecular architecture of the inner ring scaffold of the human nuclear pore complex | |||||||||
Map data | None | |||||||||
Sample |
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Method | subtomogram averaging / cryo EM / Resolution: 21.4 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_8087.map.gz | 12.6 MB | EMDB map data format | |
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Header (meta data) | emd-8087-v30.xml emd-8087.xml | 8 KB 8 KB | Display Display | EMDB header |
Images | emd_8087.png | 171 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8087 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8087 | HTTPS FTP |
-Related structure data
Related structure data | 8085C 8086C 5ijnFC 5ijoFC F: fitted*YM C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8087.map.gz / Format: CCP4 / Size: 91.1 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 : Inner ring of the nuclear pore complex
Entire | Name: Inner ring of the nuclear pore complex |
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Components |
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-Supramolecule #1: Inner ring of the nuclear pore complex
Supramolecule | Name: Inner ring of the nuclear pore complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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-Supramolecule #2: Inner ring of the Nuclear Pore complex
Supramolecule | Name: Inner ring of the Nuclear Pore complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 3.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 101 / Number images used: 11112 |
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Final angle assignment | Type: OTHER |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 21.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 8400 |