+Open data
-Basic information
Entry | Database: PDB / ID: 7n85 | ||||||||||||
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Title | Inner ring spoke from the isolated yeast NPC | ||||||||||||
Components |
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Keywords | TRANSLOCASE / nuclear pore complex / inner ring / spoke | ||||||||||||
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 / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / telomere tethering at nuclear periphery ...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 / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / telomere tethering at nuclear periphery / regulation of nucleocytoplasmic transport / nuclear pore organization / nuclear pore complex assembly / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / nuclear pore nuclear basket / RNA export from nucleus / protein localization to kinetochore / structural constituent of nuclear pore / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / regulation of mitotic nuclear division / NLS-bearing protein import into nucleus / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / mRNA transport / heterochromatin formation / nuclear pore / nuclear periphery / chromosome segregation / promoter-specific chromatin binding / phospholipid binding / protein import into nucleus / protein transport / single-stranded DNA binding / nuclear envelope / nuclear membrane / molecular adaptor activity / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.6 Å | ||||||||||||
Model details | yeast Nup84 complexes in double outer ring | ||||||||||||
Authors | Akey, C.W. / Rout, M.P. / Ouch, C. / Echevarria, I. / Fernandez-Martinez, J. / Nudelman, I. | ||||||||||||
Funding support | United States, 3items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7n85.cif.gz | 2.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7n85.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7n85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/7n85 ftp://data.pdbj.org/pub/pdb/validation_reports/n8/7n85 | HTTPS FTP |
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-Related structure data
Related structure data | 24232MC 7n84C 7n9fC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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3 |
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Symmetry | Point symmetry: (Schoenflies symbol: C8 (8 fold cyclic)) |
-Components
-Protein , 10 types, 28 molecules 0Y1ZADGJBEHKCFILMONPQRSTUWVX
#1: Protein | Mass: 169651.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38181 #2: Protein | Mass: 156827.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40064 #4: Protein | Mass: 86611.672 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14907 #5: Protein | Mass: 57547.145 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P48837 #6: Protein | Mass: 49174.762 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02199 #7: Protein | Mass: 191718.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47054 #8: Protein | Mass: 188753.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P52593 #9: Protein | Mass: 96291.586 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P34077 #10: Protein | Mass: 52688.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03790 #11: Protein | Mass: 58853.902 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q05166 |
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-Protein/peptide , 1 types, 2 molecules 56
#3: Protein/peptide | Mass: 3081.790 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
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-Details
Compound details | spoke model |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: spoke from yeast inner ring / Type: COMPLEX Details: recombined inner ring from spoke multi-body and focused 3D refinements with isolated NPC Entity ID: all / Source: NATURAL | |||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 16.0 MDa / Experimental value: YES | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Cellular location: nuclear envelope | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: inner ring spoke imaged from isolated yeast NPC | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 37651 X / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4015 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 2-40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145000 / Algorithm: FOURIER SPACE Details: 1.5x spoke from multibody and focused refinements after re-extraction of particles Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL Details: initial spoke model from PDBDEV_00000012, rigid body dock with chimera and fitting with MDFF |