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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0909 | |||||||||
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Title | core region reconstruction. | |||||||||
![]() | core region reconstruction | |||||||||
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![]() | building block of vertebrate NPC. / STRUCTURAL PROTEIN | |||||||||
Function / homology | ![]() macromolecule localization / nitrogen compound transport / GATOR2 complex / nephron development / macromolecule metabolic process / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore inner ring / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring ...macromolecule localization / nitrogen compound transport / GATOR2 complex / nephron development / macromolecule metabolic process / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore inner ring / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / nuclear pore organization / COPII vesicle coat / : / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / positive regulation of TOR signaling / mRNA transport / cellular response to nutrient levels / mRNA export from nucleus / nuclear pore / positive regulation of TORC1 signaling / cellular response to amino acid starvation / GTPase activator activity / kinetochore / protein import into nucleus / protein transport / nuclear membrane / cell division / lysosomal membrane / structural molecule activity / positive regulation of DNA-templated transcription / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.5 Å | |||||||||
![]() | Shi Y / Huang G | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex by cryo-electron microscopy single particle analysis. Authors: Gaoxingyu Huang / Yanqing Zhang / Xuechen Zhu / Chao Zeng / Qifan Wang / Qiang Zhou / Qinghua Tao / Minhao Liu / Jianlin Lei / Chuangye Yan / Yigong Shi / ![]() Abstract: The nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle ...The nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle cryo-electron microscopy (cryo-EM) structure of the CR from Xenopus laevis NPC at average resolutions of 5.5-7.9 Å, with local resolutions reaching 4.5 Å. Improved resolutions allow identification and placement of secondary structural elements in the majority of the CR components. The two Y complexes in each CR subunit interact with each other and associate with those from flanking subunits, forming a circular scaffold. Within each CR subunit, the Nup358-containing region wraps around the stems of both Y complexes, likely stabilizing the scaffold. Nup205 connects the short arms of the two Y complexes and associates with the stem of a neighboring Y complex. The Nup214-containing region uses an extended coiled-coil to link Nup85 of the two Y complexes and protrudes into the axial pore of the NPC. These previously uncharacterized structural features reveal insights into NPC assembly. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 58.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 38 KB 38 KB | Display Display | ![]() |
Images | ![]() | 46 KB | ||
Filedesc metadata | ![]() | 13 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lk8MC ![]() 0910C ![]() 0911C ![]() 0982C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | core region reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.222 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Cytoplasmic Ring Subunit of Xenopus laevis NPC
+Supramolecule #1: Cytoplasmic Ring Subunit of Xenopus laevis NPC
+Macromolecule #1: MGC83295 protein
+Macromolecule #2: Nuclear pore complex protein Nup85
+Macromolecule #3: MGC154553 protein
+Macromolecule #4: Nucleoporin SEH1-A
+Macromolecule #5: outer Nup160
+Macromolecule #6: MGC83926 protein
+Macromolecule #7: Nuclear pore complex protein Nup96
+Macromolecule #8: GATOR complex protein SEC13
+Macromolecule #9: Nuclear pore complex protein
+Macromolecule #10: outer Nup133
+Macromolecule #11: Nup358 complex, clamps
+Macromolecule #12: Nup214 complex Coiled-coil region 1, helix 1
+Macromolecule #13: Nup214 complex coiled coil region 1, helix 2
+Macromolecule #14: Nup214 complex coiled coil region 1, helix 3
+Macromolecule #15: Nup214 complex Coiled coil region 2, helix 1
+Macromolecule #16: Nup214 complex Coiled coil region 2, helix 2
+Macromolecule #17: Nup214 complex Coiled coil region 2, helix 3
+Macromolecule #18: bridge domain
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | tissue |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil / Material: COPPER |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 75.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 616547 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-6lk8: |