- EMDB-24232: Inner ring spoke from the isolated yeast NPC -
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Open data
ID or keywords:
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Basic information
Entry
Database: EMDB / ID: EMD-24232
Title
Inner ring spoke from the isolated yeast NPC
Map data
recombined full inner ring of spokes
Sample
Complex: spoke from yeast inner ring
Protein or peptide: x 11 types
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 / chromosome, subtelomeric region / 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 / chromosome, subtelomeric region / 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 / 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 / tRNA export from nucleus / protein localization to kinetochore / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / RNA export from nucleus / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / regulation of mitotic nuclear division / nuclear localization sequence binding / NLS-bearing protein import into nucleus / ribosomal large subunit export from nucleus / mRNA transport / nuclear pore / ribosomal small subunit export from nucleus / nuclear periphery / molecular condensate scaffold activity / chromosome segregation / promoter-specific chromatin binding / heterochromatin formation / phospholipid binding / protein import into nucleus / nuclear envelope / protein transport / single-stranded DNA binding / nuclear membrane / amyloid fibril formation / cell division / chromatin binding / positive regulation of DNA-templated transcription / protein-containing complex binding / DNA binding / RNA binding / identical protein binding / nucleus Similarity search - Function
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01 GM45377
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01 GM112108
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
P41 GM109824
United States
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
Deposition
Jun 13, 2021
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Header (metadata) release
Jan 26, 2022
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Map release
Jan 26, 2022
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Update
Jun 5, 2024
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Current status
Jun 5, 2024
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Name: spoke from yeast inner ring / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: recombined inner ring from spoke multi-body and focused 3D refinements with isolated NPC
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
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Electron microscopy
Microscope
FEI TITAN KRIOS
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
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