+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24231 | ||||||||||||
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Title | Double nuclear outer ring from the isolated yeast NPC | ||||||||||||
Map data | recombined double nuclear outer ring | ||||||||||||
Sample |
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Keywords | nuclear pore complex / outer ring / Nup84 complex / TRANSLOCASE | ||||||||||||
Function / homology | Function and homology information mRNA export from nucleus in response to heat stress / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / protein localization to nuclear inner membrane / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore inner ring / nuclear pore localization / regulation of nucleocytoplasmic transport ...mRNA export from nucleus in response to heat stress / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / protein localization to nuclear inner membrane / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore inner ring / nuclear pore localization / regulation of nucleocytoplasmic transport / nuclear pore central transport channel / regulation of TORC1 signaling / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / telomere tethering at nuclear periphery / nuclear pore organization / COPII vesicle coat / nuclear pore cytoplasmic filaments / positive regulation of protein exit from endoplasmic reticulum / 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 / SUMOylation of SUMOylation proteins / tRNA export from nucleus / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / RNA export from nucleus / nucleocytoplasmic transport / silent mating-type cassette heterochromatin formation / vacuolar membrane / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / ribosomal large subunit export from nucleus / subtelomeric heterochromatin formation / positive regulation of TOR signaling / mRNA transport / mRNA export from nucleus / nuclear pore / ERAD pathway / positive regulation of TORC1 signaling / protein export from nucleus / cellular response to amino acid starvation / cell periphery / protein import into nucleus / nuclear envelope / double-strand break repair / protein transport / cellular response to heat / chromosome, telomeric region / nuclear membrane / hydrolase activity / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / RNA binding / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.6 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_24231.map.gz | 390.4 MB | EMDB map data format | |
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Header (meta data) | emd-24231-v30.xml emd-24231.xml | 45.1 KB 45.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24231_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_24231.png | 132 KB | ||
Masks | emd_24231_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-24231.cif.gz | 11.2 KB | ||
Others | emd_24231_additional_1.map.gz emd_24231_additional_2.map.gz emd_24231_additional_3.map.gz emd_24231_additional_4.map.gz emd_24231_additional_5.map.gz emd_24231_half_map_1.map.gz emd_24231_half_map_2.map.gz | 392.1 MB 392.3 MB 1.5 MB 387.6 MB 390.9 MB 80.8 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24231 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24231 | HTTPS FTP |
-Validation report
Summary document | emd_24231_validation.pdf.gz | 852.4 KB | Display | EMDB validaton report |
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Full document | emd_24231_full_validation.pdf.gz | 852 KB | Display | |
Data in XML | emd_24231_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | emd_24231_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24231 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24231 | HTTPS FTP |
-Related structure data
Related structure data | 7n84MC 7n85C 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_24231.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | recombined double nuclear outer ring | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_24231_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: zoned proximal outer nuclear ring
File | emd_24231_additional_1.map | ||||||||||||
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Annotation | zoned proximal outer nuclear ring | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: zoned proximal outer nuclear ring
File | emd_24231_additional_2.map | ||||||||||||
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Annotation | zoned proximal outer nuclear ring | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: post processed multibody for double nuclear outer ring
File | emd_24231_additional_3.map | ||||||||||||
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Annotation | post processed multibody for double nuclear outer ring | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: zoned Nup188-192 density ring
File | emd_24231_additional_4.map | ||||||||||||
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Annotation | zoned Nup188-192 density ring | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: zoned putative basket density ring
File | emd_24231_additional_5.map | ||||||||||||
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Annotation | zoned putative basket density ring | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map for double Y multibody
File | emd_24231_half_map_1.map | ||||||||||||
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Annotation | half map for double Y multibody | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map for double Y multibody
File | emd_24231_half_map_2.map | ||||||||||||
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Annotation | half map for double Y multibody | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : yeast double outer ring
+Supramolecule #1: yeast double outer ring
+Macromolecule #1: Nucleoporin NUP188
+Macromolecule #2: unknown
+Macromolecule #3: Nucleoporin NUP120
+Macromolecule #4: Nucleoporin NUP85
+Macromolecule #5: Nucleoporin 145c
+Macromolecule #6: Protein transport protein SEC13
+Macromolecule #7: Nucleoporin SEH1
+Macromolecule #8: Nucleoporin NUP84
+Macromolecule #9: Nucleoporin NUP133
-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 | double outer ring 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 | molecular dynamics flexible fitting |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-7n84: |