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- EMDB-13851: Cryo-em structure of the Nup98 fibril polymorph 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-13851
TitleCryo-em structure of the Nup98 fibril polymorph 1
Map dataCryo-em structure of the Nup98 fibril polymorph 1
Sample
  • Complex: The nuclear pore complex protein Nup98 fibril polymorph 1
    • Protein or peptide: Nuclear pore complex protein Nup98
KeywordsNuclear pore complex protein Nup98 functional amyloid fibril PROTEIN FIBRIL / PROTEIN FIBRIL
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 / Transport of Ribonucleoproteins into the Host Nucleus ...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 / 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 / NS1 Mediated Effects on Host Pathways / Transport of the SLBP Dependant Mature mRNA / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / nuclear localization sequence binding / 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 / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / 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 / Mitotic Prometaphase / serine-type peptidase activity / 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 / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / ISG15 antiviral mechanism / molecular condensate scaffold activity / Separation of Sister Chromatids / HCMV Early Events / 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
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)
Methodhelical reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsIbanez de Opakua A / Geraets JA
Funding support Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)787679 Germany
German Research Foundation (DFG)656281 Germany
CitationJournal: Nat.Chem. / Year: 2022
Title: Molecular interactions of FG nucleoporin repeats at high resolution.
Authors: Ibanez de Opakua A / Geraets JA / Frieg B / Dienemann C / Savastano A / Rankovic M / Cima-Omori MS / Schroder GF / Zweckstetter M
History
DepositionNov 5, 2021-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_13851.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-em structure of the Nup98 fibril polymorph 1
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.15932423 - 0.3104888
Average (Standard dev.)0.0007100354 (±0.012944809)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 262.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The nuclear pore complex protein Nup98 fibril polymorph 1

EntireName: The nuclear pore complex protein Nup98 fibril polymorph 1
Components
  • Complex: The nuclear pore complex protein Nup98 fibril polymorph 1
    • Protein or peptide: Nuclear pore complex protein Nup98

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Supramolecule #1: The nuclear pore complex protein Nup98 fibril polymorph 1

SupramoleculeName: The nuclear pore complex protein Nup98 fibril polymorph 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The Nup98 polymorph 1 fibril is formed by three protofilaments, consisting of Nup98 monomers.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Nuclear pore complex protein Nup98

MacromoleculeName: Nuclear pore complex protein Nup98 / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.005211 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
TGTANTLFGT ASTGTSLFSS QNNAFAQNKP TGFGNFGTST

UniProtKB: Nuclear pore complex protein Nup98-Nup96

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 4180 / Average exposure time: 2.557 sec. / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.65 Å
Applied symmetry - Helical parameters - Δ&Phi: -3.09 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 71697
Segment selectionNumber selected: 356482
Startup modelType of model: OTHER / Details: featureless cylinder
Final angle assignmentType: NOT APPLICABLE

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