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 / regulation of TORC1 signaling / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore organization / tRNA export from nucleus / 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 / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / RNA export from nucleus / SUMOylation of chromatin organization proteins / 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 / positive regulation of TOR signaling / subtelomeric heterochromatin formation / mRNA transport / mRNA export from nucleus / nuclear pore / ERAD pathway / positive regulation of TORC1 signaling / cellular response to amino acid starvation / protein export from nucleus / cell periphery / protein import into nucleus / double-strand break repair / protein transport / nuclear envelope / nuclear membrane / chromosome, telomeric region / hydrolase activity / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / 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
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
Protein or peptide: Protein transport protein SEC13
Protein or peptide: Nucleoporin SEH1
Protein or peptide: Nucleoporin NUP84
Protein or peptide: Nucleoporin NUP133
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Supramolecule #1: yeast double outer ring
Supramolecule
Name: yeast double outer ring / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Novel outer ring C8 protomer with two copies of Nup84 complex, one copy of Nup188 and an unknown basket anchor model
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
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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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