+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24232 | ||||||||||||
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Title | Inner ring spoke from the isolated yeast NPC | ||||||||||||
Map data | recombined full inner ring of spokes | ||||||||||||
Sample |
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Keywords | nuclear pore complex / inner ring / spoke / TRANSLOCASE | ||||||||||||
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 / protein localization to nuclear inner membrane / nuclear pore inner ring / regulation of nucleocytoplasmic transport / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery ...response to spindle checkpoint signaling / nuclear pore linkers / : / regulation of protein desumoylation / mRNA export from nucleus in response to heat stress / protein localization to nuclear inner membrane / nuclear pore inner ring / regulation of nucleocytoplasmic transport / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore complex assembly / nuclear pore organization / tRNA export from nucleus / nuclear pore cytoplasmic filaments / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / protein localization to kinetochore / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / RNA export from nucleus / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / regulation of mitotic nuclear division / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / 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: 7.6 Å | ||||||||||||
Authors | Akey CW / Rout MP | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Cell / Year: 2022 Title: Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Authors: Christopher W Akey / Digvijay Singh / Christna Ouch / Ignacia Echeverria / Ilona Nudelman / Joseph M Varberg / Zulin Yu / Fei Fang / Yi Shi / Junjie Wang / Daniel Salzberg / Kangkang Song / ...Authors: Christopher W Akey / Digvijay Singh / Christna Ouch / Ignacia Echeverria / Ilona Nudelman / Joseph M Varberg / Zulin Yu / Fei Fang / Yi Shi / Junjie Wang / Daniel Salzberg / Kangkang Song / Chen Xu / James C Gumbart / Sergey Suslov / Jay Unruh / Sue L Jaspersen / Brian T Chait / Andrej Sali / Javier Fernandez-Martinez / Steven J Ludtke / Elizabeth Villa / Michael P Rout / Abstract: Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the isolated yeast NPC in which the inner ring is resolved by cryo-EM at sub- ...Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the isolated yeast NPC in which the inner ring is resolved by cryo-EM at sub-nanometer resolution to show how flexible connectors tie together different structural and functional layers. These connectors may be targets for phosphorylation and regulated disassembly in cells with an open mitosis. Moreover, some nucleoporin pairs and transport factors have similar interaction motifs, which suggests an evolutionary and mechanistic link between assembly and transport. We provide evidence for three major NPC variants that may foreshadow functional specializations at the nuclear periphery. Cryo-electron tomography extended these studies, providing a model of the in situ NPC with a radially expanded inner ring. Our comprehensive model reveals features of the nuclear basket and central transporter, suggests a role for the lumenal Pom152 ring in restricting dilation, and highlights structural plasticity that may be required for transport. | ||||||||||||
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_24232.map.gz | 29.4 MB | EMDB map data format | |
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Header (meta data) | emd-24232-v30.xml emd-24232.xml | 43.7 KB 43.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24232_fsc.xml | 12.2 KB | Display | FSC data file |
Images | emd_24232.png | 216.9 KB | ||
Masks | emd_24232_msk_1.map | 71.8 MB | Mask map | |
Filedesc metadata | emd-24232.cif.gz | 13 KB | ||
Others | emd_24232_additional_1.map.gz emd_24232_additional_2.map.gz emd_24232_half_map_1.map.gz emd_24232_half_map_2.map.gz | 2.1 MB 44.1 MB 55.9 MB 55.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24232 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24232 | HTTPS FTP |
-Validation report
Summary document | emd_24232_validation.pdf.gz | 801.1 KB | Display | EMDB validaton report |
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Full document | emd_24232_full_validation.pdf.gz | 800.6 KB | Display | |
Data in XML | emd_24232_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_24232_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24232 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24232 | HTTPS FTP |
-Related structure data
Related structure data | 7n85MC 7n84C 7n9fC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24232.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | recombined full inner ring of spokes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.66 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_24232_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: zoned single spoke
File | emd_24232_additional_1.map | ||||||||||||
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Annotation | zoned single spoke | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: post-process focused spoke refinement after multibody
File | emd_24232_additional_2.map | ||||||||||||
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Annotation | post-process focused spoke refinement after multibody | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map focused spoke refinement
File | emd_24232_half_map_1.map | ||||||||||||
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Annotation | half map focused spoke refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map focused spoke refinement
File | emd_24232_half_map_2.map | ||||||||||||
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Annotation | half map focused spoke refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : spoke from yeast inner ring
+Supramolecule #1: spoke from yeast inner ring
+Macromolecule #1: Nucleoporin NUP170
+Macromolecule #2: Nucleoporin NUP157
+Macromolecule #3: Unknown connectors
+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 ASM4
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | |||||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK III | |||||||||||||||||||||
Details | inner ring spoke imaged from isolated yeast NPC |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.8000000000000003 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 37651 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 50000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | initial spoke model from PDBDEV_00000012, rigid body dock with chimera and fitting with MDFF |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-7n85: |