nuclear pore complex / nucleocytoplasmic transport / nucleoporin / membrane protein / translocase / TRANSPORT PROTEIN
Function / homology
Function and homology information
response to spindle checkpoint signaling / nuclear pore linkers / regulation of protein desumoylation / mRNA export from nucleus in response to heat stress / protein localization to nuclear inner membrane / nuclear pore inner ring / regulation of nucleocytoplasmic transport / chromosome, subtelomeric region / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery ...response to spindle checkpoint signaling / nuclear pore linkers / regulation of protein desumoylation / mRNA export from nucleus in response to heat stress / protein localization to nuclear inner membrane / nuclear pore inner ring / regulation of nucleocytoplasmic transport / chromosome, subtelomeric region / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore complex assembly / nuclear pore organization / nuclear pore cytoplasmic filaments / 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 / 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 / poly(A)+ mRNA export from nucleus / regulation of mitotic nuclear division / nuclear localization sequence binding / NLS-bearing protein import into nucleus / ribosomal large subunit export from nucleus / mRNA transport / nuclear pore / ribosomal small subunit export from nucleus / nuclear periphery / molecular condensate scaffold activity / chromosome segregation / promoter-specific chromatin binding / heterochromatin formation / phospholipid binding / protein import into nucleus / protein transport / nuclear envelope / single-stranded DNA binding / nuclear membrane / amyloid fibril formation / cell division / chromatin binding / protein-containing complex binding / positive regulation of DNA-templated transcription / DNA binding / RNA binding / identical protein binding / nucleus Similarity search - Function
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
NIH R01 GM45377
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
NIH P41 GM109824
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
NIH R01 GM112108
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
NIH GM117212
United States
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.
Type of model: OTHER Details: C8 symmetrized NPC map segmented in CHIMERA with Segger to provide initial 3D map of the double outer ring, which was low pass filtered for the first reference.
Final reconstruction
Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) Details: Multibody extracted spoke image stack processed in CryoSPARC Number images used: 208392
Initial angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7) / Details: C1 symmetry used with Multibody particles
Final angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2) / Software - details: non-uniform refinement Details: C1 symmetry used to refine inner ring spoke with appropriate mask
Final 3D classification
Software - Name: RELION (ver. 3.0.7)
FSC plot (resolution estimation)
-
Atomic model buiding 1
Initial model
Chain - Source name: Other / Chain - Initial model type: experimental model / Details: none
Details
Rigid body docking of 3D map of Nucleoporins in the spoke complex with Chimera followed by flexible fitting and rebuilding in Coot.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi