+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41116 | |||||||||||||||
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Title | Lumenal ring of the isolated yeast NPC | |||||||||||||||
Map data | Main map reconstructed from Multibody volume | |||||||||||||||
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: 14.7 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
Map data | emd_41116.map.gz | 325.5 MB | EMDB map data format | |
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Header (meta data) | emd-41116-v30.xml emd-41116.xml | 27.7 KB 27.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41116_fsc.xml | 21.8 KB | Display | FSC data file |
Images | emd_41116.png | 67.5 KB | ||
Filedesc metadata | emd-41116.cif.gz | 6 KB | ||
Others | emd_41116_additional_1.map.gz emd_41116_additional_2.map.gz emd_41116_additional_3.map.gz emd_41116_half_map_1.map.gz emd_41116_half_map_2.map.gz | 1 MB 3.3 MB 1 MB 18.1 MB 18.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41116 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41116 | HTTPS FTP |
-Validation report
Summary document | emd_41116_validation.pdf.gz | 477.8 KB | Display | EMDB validaton report |
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Full document | emd_41116_full_validation.pdf.gz | 477.3 KB | Display | |
Data in XML | emd_41116_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | emd_41116_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41116 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41116 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41116.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Main map reconstructed from Multibody volume | ||||||||||||||||||||
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
-Additional map: multibody half map
File | emd_41116_additional_1.map | ||||||||||||
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Annotation | multibody half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: post processed multibody volume bf -300 local resolution box 50
File | emd_41116_additional_2.map | ||||||||||||
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Annotation | post processed multibody volume bf -300 local resolution box 50 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: multibody half map
File | emd_41116_additional_3.map | ||||||||||||
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Annotation | multibody half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map full D8 lumenal ring
File | emd_41116_half_map_1.map | ||||||||||||
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Annotation | half map full D8 lumenal ring | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map full D8 lumenal ring
File | emd_41116_half_map_2.map | ||||||||||||
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Annotation | half map full D8 lumenal ring | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Lumenal rig of Nuclear Pore Complex
Entire | Name: Lumenal rig of Nuclear Pore Complex |
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Components |
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-Supramolecule #1: Lumenal rig of Nuclear Pore Complex
Supramolecule | Name: Lumenal rig of 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 - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK III |
Details | One step affinity purified with NPC |
-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 | The 2x protomer was fitted together to form a complete c8 lumenal ring with imposed 2-fold symmetry. |
Refinement | Space: REAL / Protocol: OTHER / Target criteria: cross correlation |