+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41123 | |||||||||||||||
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Title | Composite multiscale structure of the yeast NPC | |||||||||||||||
Map data | One possible Master map | |||||||||||||||
Sample |
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Keywords | nuclear pore complex / nucleocytoplasmic transport / nucleoporin / membrane protein / TRANSPORT PROTEIN | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 28.0 Å | |||||||||||||||
Authors | Akey CW / Echeverria I / Ouch C / Fernandez-Martinez J / Rout MP | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Mol Cell / Year: 2023 Title: Implications of a multiscale structure of the yeast nuclear pore complex. Authors: Christopher W Akey / Ignacia Echeverria / Christna Ouch / Ilona Nudelman / Yi Shi / Junjie Wang / Brian T Chait / Andrej Sali / Javier Fernandez-Martinez / Michael P Rout / Abstract: Nuclear pore complexes (NPCs) direct the nucleocytoplasmic transport of macromolecules. Here, we provide a composite multiscale structure of the yeast NPC, based on improved 3D density maps from ...Nuclear pore complexes (NPCs) direct the nucleocytoplasmic transport of macromolecules. Here, we provide a composite multiscale structure of the yeast NPC, based on improved 3D density maps from cryogenic electron microscopy and AlphaFold2 models. Key features of the inner and outer rings were integrated into a comprehensive model. We resolved flexible connectors that tie together the core scaffold, along with equatorial transmembrane complexes and a lumenal ring that anchor this channel within the pore membrane. The organization of the nuclear double outer ring reveals an architecture that may be shared with ancestral NPCs. Additional connections between the core scaffold and the central transporter suggest that under certain conditions, a degree of local organization is present at the periphery of the transport machinery. These connectors may couple conformational changes in the scaffold to the central transporter to modulate transport. Collectively, this analysis provides insights into assembly, transport, and NPC evolution. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
-Validation report
Summary document | emd_41123_validation.pdf.gz | 943 KB | Display | EMDB validaton report |
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Full document | emd_41123_full_validation.pdf.gz | 942.6 KB | Display | |
Data in XML | emd_41123_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | emd_41123_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41123 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41123 | HTTPS FTP |
-Related 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_41123.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | One possible Master map | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.66 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
+Mask #1
+Additional map: Nsp1 inner c8 ring
+Additional map: cytoplasmic outer ring c8 ring
+Additional map: segmented distal Y-complex nuclear outer ring
+Additional map: segmented proximal Y-complex nuclear outer ring
+Additional map: molmap model for inner copy of putative Nup188-192 c8 ring
+Additional map: molmap model for outer copy of putative Nup188-192 c8 ring
+Additional map: segmented densities for two putative Nic96 CTDs - c8 ring
+Additional map: L2 linker domains - c8 ring
+Additional map: L1 linker domains - c8 ring
+Additional map: segmented central transporter-plug, effectively a cylindrical average
+Additional map: Membrane interacting c8 ring
+Additional map: adaptin-like c8 ring
+Additional map: segmented Nic96 NTD connectors map-c8 ring
+Additional map: segmented new connectors map-c8 ring
+Additional map: segmented Pom34-152 TMD map-c8 ring
+Additional map: segmented Ndc1 TMD map-c8 ring
+Additional map: segmented micelle map-c8 ring
+Additional map: lumenal c8 ring
+Half map: #2
+Half map: #1
-Sample components
-Entire : Nuclear Pore Complex
Entire | Name: Nuclear Pore Complex |
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Components |
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-Supramolecule #1: Nuclear Pore Complex
Supramolecule | Name: Nuclear Pore Complex / type: complex / ID: 1 / Parent: 0 / Details: Protein A tagged Mlp1 pullout of NPC |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) Strain: MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 MLP1-PPX-ProteinA::HIS5 Organelle: nucleus / Location in cell: nuclear envelope |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.5 Details: 20mM HEPES,50mM Potassium acetate,20mM NaCl,2mM MgCl2,1mM DTT |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK III |
Details | One step affinity purified |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Details | Preliminary grid screening done manually with individual images of low magnification montages of candidate meshes. |
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 / Details: 3218 images retained after triage |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 37651 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: Other / Chain - Initial model type: experimental model / Details: none |
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Details | Rigid body docking of 3D maps with Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross correlation |