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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 organization / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus ...nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / 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 / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / Postmitotic nuclear pore complex (NPC) reformation / positive regulation of mRNA splicing, via spliceosome / 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 / nuclear pore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / 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 / promoter-specific chromatin binding / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / molecular condensate scaffold activity / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / 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 / Nucleoporin autopeptidase / 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: Alain Ibáñez de Opakua / James A Geraets / Benedikt Frieg / Christian Dienemann / Adriana Savastano / Marija Rankovic / Maria-Sol Cima-Omori / Gunnar F Schröder / Markus Zweckstetter /
Abstract: Proteins that contain repeat phenylalanine-glycine (FG) residues phase separate into oncogenic transcription factor condensates in malignant leukaemias, form the permeability barrier of the nuclear ...Proteins that contain repeat phenylalanine-glycine (FG) residues phase separate into oncogenic transcription factor condensates in malignant leukaemias, form the permeability barrier of the nuclear pore complex and mislocalize in neurodegenerative diseases. Insights into the molecular interactions of FG-repeat nucleoporins have, however, remained largely elusive. Using a combination of NMR spectroscopy and cryoelectron microscopy, we have identified uniformly spaced segments of transient β-structure and a stable preformed α-helix recognized by messenger RNA export factors in the FG-repeat domain of human nucleoporin 98 (Nup98). In addition, we have determined at high resolution the molecular organization of reversible FG-FG interactions in amyloid fibrils formed by a highly aggregation-prone segment in Nup98. We have further demonstrated that amyloid-like aggregates of the FG-repeat domain of Nup98 have low stability and are reversible. Our results provide critical insights into the molecular interactions underlying the self-association and phase separation of FG-repeat nucleoporins in physiological and pathological cell activities.
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

Supplemental images

emd_13851.png

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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 250 pix.
= 262.5 Å		1.05 Å/pix.
x 250 pix.
= 262.5 Å		1.05 Å/pix.
x 250 pix.
= 262.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
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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Half map: Cryo-em structure of the Nup98 fibril polymorph 1, half map 2

Fileemd_13851_half_map_1.map
AnnotationCryo-em structure of the Nup98 fibril polymorph 1, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-em structure of the Nup98 fibril polymorph 1, half map 1

Fileemd_13851_half_map_2.map
AnnotationCryo-em structure of the Nup98 fibril polymorph 1, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
FSC plot (resolution estimation)

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