+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41300 | |||||||||||||||
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Title | Inner spoke ring of the yeast NPC | |||||||||||||||
Map data | c8 inner spoke ring recombined from multibody | |||||||||||||||
Sample |
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Keywords | nuclear pore complex / nucleocytoplasmic transport / nucleoporin / membrane protein / translocase / TRANSPORT PROTEIN | |||||||||||||||
Function / homology | Function and homology information response to spindle checkpoint signaling / nuclear pore linkers / : / regulation of protein desumoylation / mRNA export from nucleus in response to heat stress / nuclear pore inner ring / protein localization to nuclear inner membrane / telomere tethering at nuclear periphery / regulation of nucleocytoplasmic transport / nuclear pore central transport channel ...response to spindle checkpoint signaling / nuclear pore linkers / : / regulation of protein desumoylation / mRNA export from nucleus in response to heat stress / nuclear pore inner ring / protein localization to nuclear inner membrane / telomere tethering at nuclear periphery / regulation of nucleocytoplasmic transport / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear pore complex assembly / nuclear pore cytoplasmic filaments / tRNA export from nucleus / Regulation of HSF1-mediated heat shock response / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / protein localization to kinetochore / structural constituent of nuclear pore / RNA export from nucleus / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / nuclear localization sequence binding / poly(A)+ mRNA export from nucleus / regulation of mitotic nuclear division / NLS-bearing protein import into nucleus / ribosomal large subunit export from nucleus / mRNA transport / ribosomal small subunit export from nucleus / heterochromatin formation / nuclear pore / nuclear periphery / molecular condensate scaffold activity / chromosome segregation / promoter-specific chromatin binding / phospholipid binding / protein import into nucleus / protein transport / nuclear envelope / single-stranded DNA binding / nuclear membrane / amyloid fibril formation / cell cycle / cell division / chromatin binding / protein-containing complex binding / positive regulation of DNA-templated transcription / DNA binding / RNA binding / identical protein binding / nucleus Similarity search - Function | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||||||||
Authors | Akey CW / Echeverria I / Ouch C / Fernandez-Martinez J / Rout MP | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Mol Cell / Year: 2023 Title: Implications of a multiscale structure of the yeast nuclear pore complex. Authors: Christopher W Akey / Ignacia Echeverria / Christna Ouch / Ilona Nudelman / Yi Shi / Junjie Wang / Brian T Chait / Andrej Sali / Javier Fernandez-Martinez / Michael P Rout / Abstract: Nuclear pore complexes (NPCs) direct the nucleocytoplasmic transport of macromolecules. Here, we provide a composite multiscale structure of the yeast NPC, based on improved 3D density maps from ...Nuclear pore complexes (NPCs) direct the nucleocytoplasmic transport of macromolecules. Here, we provide a composite multiscale structure of the yeast NPC, based on improved 3D density maps from cryogenic electron microscopy and AlphaFold2 models. Key features of the inner and outer rings were integrated into a comprehensive model. We resolved flexible connectors that tie together the core scaffold, along with equatorial transmembrane complexes and a lumenal ring that anchor this channel within the pore membrane. The organization of the nuclear double outer ring reveals an architecture that may be shared with ancestral NPCs. Additional connections between the core scaffold and the central transporter suggest that under certain conditions, a degree of local organization is present at the periphery of the transport machinery. These connectors may couple conformational changes in the scaffold to the central transporter to modulate transport. Collectively, this analysis provides insights into assembly, transport, and NPC evolution. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41300.map.gz | 15.1 MB | EMDB map data format | |
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Header (meta data) | emd-41300-v30.xml emd-41300.xml | 46.8 KB 46.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41300_fsc.xml | 21.8 KB | Display | FSC data file |
Images | emd_41300.png | 205.6 KB | ||
Filedesc metadata | emd-41300.cif.gz | 13.7 KB | ||
Others | emd_41300_additional_1.map.gz emd_41300_additional_2.map.gz emd_41300_additional_3.map.gz emd_41300_half_map_1.map.gz emd_41300_half_map_2.map.gz | 51.2 MB 51.2 MB 2.4 MB 27 MB 27.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41300 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41300 | HTTPS FTP |
-Related structure data
Related structure data | 8tj5MC 8t9lC 8tieC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41300.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | c8 inner spoke ring recombined from multibody | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.66 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: spoke multibody half map
File | emd_41300_additional_1.map | ||||||||||||
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Annotation | spoke multibody half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: spoke multibody half map
File | emd_41300_additional_2.map | ||||||||||||
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Annotation | spoke multibody half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: c2 spoke map aligned within c8 ring and aligned with pdb
File | emd_41300_additional_3.map | ||||||||||||
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Annotation | c2 spoke map aligned within c8 ring and aligned with pdb | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map of c8 spoke inner ring
File | emd_41300_half_map_1.map | ||||||||||||
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Annotation | half map of c8 spoke inner ring | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map of c8 spoke inner ring
File | emd_41300_half_map_2.map | ||||||||||||
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Annotation | half map of c8 spoke inner ring | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Nuclear Pore Complex
+Supramolecule #1: Nuclear Pore Complex
+Macromolecule #1: Spoke connector
+Macromolecule #2: Nucleoporin NUP170
+Macromolecule #3: Nucleoporin NUP157
+Macromolecule #4: Nucleoporin NSP1
+Macromolecule #5: Nucleoporin NUP57
+Macromolecule #6: Nucleoporin NUP49/NSP49
+Macromolecule #7: Nucleoporin NUP192
+Macromolecule #8: Nucleoporin NUP188
+Macromolecule #9: Nucleoporin NIC96
+Macromolecule #10: Nucleoporin NUP53
+Macromolecule #11: Nucleoporin 59
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.5 Details: 20mM HEPES,50mM Potassium acetate,20mM NaCl,2mM MgCl2,1mM DTT |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK III |
Details | One step affinity purified |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 37651 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Details | Preliminary grid screening done manually with individual images of low magnification montages of candidate meshes. |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 2-40 / Number grids imaged: 1 / Number real images: 4015 / Average electron dose: 40.0 e/Å2 / Details: 3218 images retained after triage |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: Other / Chain - Initial model type: experimental model / Details: none |
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Details | Rigid body docking of 3D map of Nucleoporins in the spoke complex with Chimera followed by flexible fitting and rebuilding in Coot. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-8tj5: |