+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16671 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the Nup98(298-327) fibril | |||||||||
Map data | Post-processed and masked map. | |||||||||
Sample |
| |||||||||
Keywords | Nup98 / nuclear pore / FG repeats / amyloid fibrils / PROTEIN FIBRIL | |||||||||
Function / homology | Function and homology information telomere tethering at nuclear periphery / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus ...telomere tethering at nuclear periphery / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / tRNA processing in the nucleus / positive regulation of mRNA splicing, via spliceosome / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / molecular condensate scaffold activity / RHO GTPases Activate Formins / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / Separation of Sister Chromatids / protein import into nucleus / nuclear envelope / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / ribonucleoprotein complex / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.67 Å | |||||||||
Authors | Ibanez de Opakua A / Cima-Omori S / Dienemann C / Zweckstetter M | |||||||||
Funding support | European Union, 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2024 Title: Impact of distinct FG nucleoporin repeats on Nup98 self-association. Authors: Alain Ibáñez de Opakua / Christian F Pantoja / Maria-Sol Cima-Omori / Christian Dienemann / Markus Zweckstetter / Abstract: Nucleoporins rich in phenylalanine/glycine (FG) residues form the permeability barrier within the nuclear pore complex and are implicated in several pathological cellular processes, including ...Nucleoporins rich in phenylalanine/glycine (FG) residues form the permeability barrier within the nuclear pore complex and are implicated in several pathological cellular processes, including oncogenic fusion condensates. The self-association of FG-repeat proteins and interactions between FG-repeats play a critical role in these activities by forming hydrogel-like structures. Here we show that mutation of specific FG repeats of Nup98 can strongly decrease the protein's self-association capabilities. We further present a cryo-electron microscopy structure of a Nup98 peptide fibril with higher stability per residue compared with previous Nup98 fibril structures. The high-resolution structure reveals zipper-like hydrophobic patches which contain a GLFG motif and are less compatible for binding to nuclear transport receptors. The identified distinct molecular properties of different regions of the nucleoporin may contribute to spatial variations in the self-association of FG-repeats, potentially influencing transport processes through the nuclear pore. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_16671.map.gz | 2.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-16671-v30.xml emd-16671.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16671_fsc.xml | 8 KB | Display | FSC data file |
Images | emd_16671.png | 118.6 KB | ||
Filedesc metadata | emd-16671.cif.gz | 4.6 KB | ||
Others | emd_16671_half_map_1.map.gz emd_16671_half_map_2.map.gz | 32.9 MB 32.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16671 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16671 | HTTPS FTP |
-Related structure data
Related structure data | 8ci8MC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_16671.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Post-processed and masked map. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: Relion refinement half map 2.
File | emd_16671_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Relion refinement half map 2. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Relion refinement half map 1.
File | emd_16671_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Relion refinement half map 1. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Nup98(298-327)
Entire | Name: Nup98(298-327) |
---|---|
Components |
|
-Supramolecule #1: Nup98(298-327)
Supramolecule | Name: Nup98(298-327) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Synthetic peptide (N-terminal acetylated and C-terminal amydated). |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Nuclear pore complex protein Nup98
Macromolecule | Name: Nuclear pore complex protein Nup98 / type: protein_or_peptide / ID: 1 / Number of copies: 25 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 3.034271 KDa |
Sequence | String: TGFSFGNTST IGQPSTNTMG LFGVTQASQP UniProtKB: Nuclear pore complex protein Nup98-Nup96 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.5 / Details: In water. |
---|---|
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.3 sec. / Average electron dose: 40.62 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Software | Name: Coot |
---|---|
Output model | PDB-8ci8: |