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- PDB-8ci8: Cryo-EM structure of the Nup98(298-327) fibril -

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Basic information

Entry
Database: PDB / ID: 8ci8
TitleCryo-EM structure of the Nup98(298-327) fibril
ComponentsNuclear pore complex protein Nup98
KeywordsPROTEIN FIBRIL / Nup98 / nuclear pore / FG repeats / amyloid fibrils
Function / homology
Function and homology information


nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore organization / 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 / Regulation of Glucokinase by Glucokinase Regulatory Protein ...nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore organization / 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 / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / nuclear localization sequence binding / structural constituent of nuclear pore / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of mRNA splicing, via spliceosome / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / 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 / nuclear pore / SUMOylation of DNA damage response and repair proteins / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / serine-type peptidase activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / nuclear periphery / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / HCMV Late Events / promoter-specific chromatin binding / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / ISG15 antiviral mechanism / protein import into nucleus / HCMV Early Events / Separation of Sister Chromatids / 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
Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile.
Similarity search - Domain/homology
Nuclear pore complex protein Nup98-Nup96
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsIbanez de Opakua, A. / Cima-Omori, S. / Dienemann, C. / Zweckstetter, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)787679European Union
CitationJournal: 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
DepositionFeb 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear pore complex protein Nup98
B: Nuclear pore complex protein Nup98
C: Nuclear pore complex protein Nup98
D: Nuclear pore complex protein Nup98
E: Nuclear pore complex protein Nup98
F: Nuclear pore complex protein Nup98
G: Nuclear pore complex protein Nup98
H: Nuclear pore complex protein Nup98
I: Nuclear pore complex protein Nup98
J: Nuclear pore complex protein Nup98
K: Nuclear pore complex protein Nup98
L: Nuclear pore complex protein Nup98
M: Nuclear pore complex protein Nup98
N: Nuclear pore complex protein Nup98
O: Nuclear pore complex protein Nup98
P: Nuclear pore complex protein Nup98
Q: Nuclear pore complex protein Nup98
R: Nuclear pore complex protein Nup98
S: Nuclear pore complex protein Nup98
T: Nuclear pore complex protein Nup98
U: Nuclear pore complex protein Nup98
V: Nuclear pore complex protein Nup98
W: Nuclear pore complex protein Nup98
X: Nuclear pore complex protein Nup98
Y: Nuclear pore complex protein Nup98


Theoretical massNumber of molelcules
Total (without water)75,85725
Polymers75,85725
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, The fibrils are formed by layers of 5 peptides separated by 4.71 Angstroms and twisted -1.19 degrees. The provided matrix represents this transformation.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide ...
Nuclear pore complex protein Nup98 / 98 kDa nucleoporin / Nucleoporin Nup98 / Nup98


Mass: 3034.271 Da / Num. of mol.: 25 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P52948

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Nup98(298-327) / Type: COMPLEX
Details: Synthetic peptide (N-terminal acetylated and C-terminal amydated).
Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6.5 / Details: In water.
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 2.3 sec. / Electron dose: 40.62 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1crYOLOparticle selection
4RELION3.1CTF correction
12RELION3.1classificationFinal classification software
13Cootmodel fitting
14PHENIXmodel refinement
15RELION3.13D reconstructionFinal reconstruction software
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.19 ° / Axial rise/subunit: 4.71 Å / Axial symmetry: C1
3D reconstructionResolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38099 / Symmetry type: HELICAL

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