+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-24258 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the in situ yeast NPC | ||||||||||||||||||||||||
![]() | full in situ NPC map recombined from 90 degree wedge focused alignment | ||||||||||||||||||||||||
![]() |
| ||||||||||||||||||||||||
![]() | NPC / nucleocytoplasmic transport / TRANSLOCASE | ||||||||||||||||||||||||
Function / homology | ![]() response to spindle checkpoint signaling / nuclear pore linkers / regulation of protein desumoylation / peroxisomal importomer complex / 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 ...response to spindle checkpoint signaling / nuclear pore linkers / regulation of protein desumoylation / peroxisomal importomer complex / 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 / adenyl-nucleotide exchange factor activity / regulation of nucleocytoplasmic transport / establishment of mitotic spindle localization / chromosome, subtelomeric region / nuclear pore central transport channel / regulation of TORC1 signaling / nuclear migration along microtubule / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / telomere tethering at nuclear periphery / nuclear pore complex assembly / 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 / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / tRNA export from nucleus / cytoplasmic dynein complex / 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 / silent mating-type cassette heterochromatin formation / vacuolar membrane / poly(A)+ mRNA export from nucleus / regulation of mitotic nuclear division / nuclear localization sequence binding / dynein intermediate chain binding / NLS-bearing protein import into nucleus / cytoplasmic microtubule / establishment of mitotic spindle orientation / 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 / ribosomal small subunit export from nucleus / ERAD pathway / Neutrophil degranulation / positive regulation of TORC1 signaling / protein export from nucleus / cellular response to amino acid starvation / nuclear periphery / molecular condensate scaffold activity / chromosome segregation / cell periphery / promoter-specific chromatin binding / heterochromatin formation / phospholipid binding / protein import into nucleus / transcription corepressor activity / double-strand break repair / protein transport / nuclear envelope / single-stranded DNA binding / cellular response to heat / nuclear membrane / amyloid fibril formation / chromosome, telomeric region / hydrolase activity / cell division / chromatin binding / endoplasmic reticulum membrane / protein-containing complex binding / 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 / DNA binding / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 37.0 Å | ||||||||||||||||||||||||
![]() | Villa E / Singh D | ||||||||||||||||||||||||
Funding support | ![]()
| ||||||||||||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 76.1 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 68.6 KB 68.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.8 KB | Display | ![]() |
Images | ![]() | 197.2 KB | ||
Masks | ![]() ![]() ![]() | 34.3 MB 34.3 MB 34.3 MB | ![]() | |
Filedesc metadata | ![]() | 18.9 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 111 MB 111.7 MB 113.8 MB 111.9 MB 111.8 MB 111.2 MB 112.2 MB 12.7 MB 12.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n9fMC ![]() 7n84C ![]() 7n85C C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | full in situ NPC map recombined from 90 degree wedge focused alignment | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.74 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
+Mask #1
+Mask #2
+Mask #3
+Additional map: zoned 3D map of Nsp1-FG-connections
+Additional map: zoned 3D map of inner ring of spokes
+Additional map: full in situ NPC map recombined from 90...
+Additional map: zoned 3D map of the N-ring
+Additional map: zoned 3D map of C-ring plus Nup82 complex with 3 Dyn 2 dimers
+Additional map: zoned 3D map of Pom152 ring
+Additional map: difference map for pore membrane
+Half map: half map
+Half map: half map
-
Sample components
+Entire : yeast NPC
+Supramolecule #1: yeast NPC
+Macromolecule #1: Nucleoporin NUP170
+Macromolecule #2: Nucleoporin NUP157
+Macromolecule #3: orphans bound to Nup192 NTD
+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
+Macromolecule #12: Nucleoporin NUP82
+Macromolecule #13: Nucleoporin NUP159
+Macromolecule #14: Nucleoporin NUP120
+Macromolecule #15: Nucleoporin NUP85
+Macromolecule #16: Nucleoporin 145c
+Macromolecule #17: Protein transport protein SEC13
+Macromolecule #18: Nucleoporin SEH1
+Macromolecule #19: Nucleoporin NUP84
+Macromolecule #20: Nucleoporin NUP133
+Macromolecule #21: Dynein light chain 1, cytoplasmic
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | subtomogram averaging |
Aggregation state | cell |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Pressure: 0.039 kPa |
Vitrification | Cryogen name: ETHANE-PROPANE Details: A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich). |
Details | W303 yeast cells were harvested during log-phase growth and diluted to an 0.8 x 107 cells/mL in YPD media. Five uL of this diluted sample was applied to glow-discharged 200-mesh, Quantafoil R2/1 grids (Electron Microscopy Sciences), excess media was manually blotted from the grid back side (opposite to the carbon substrate where the cells were deposited) and the grid was plunge frozen in a liquid ethane-propane mixture (50/50 volume, Airgas) then cryogenic, FIB milling was performed in an Aquilos DualBeam (Thermo Fisher Scientific) |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Details | Tilt series collection: dose-symmetric & bi-directional |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3708 pixel / Average exposure time: 2.0 sec. / Average electron dose: 4.5 e/Å2 Details: Images were collected in movie-mode at ~8 frames per second |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 6.0 µm / Calibrated defocus min: 2.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 42000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Details | Manual docking and limited molecular dynamics flexible fitting |
---|---|
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: cross-correlation |
Output model | ![]() PDB-7n9f: |