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- EMDB-16671: Cryo-EM structure of the Nup98(298-327) fibril -

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Basic information

Entry
Database: EMDB / ID: EMD-16671
TitleCryo-EM structure of the Nup98(298-327) fibril
Map dataPost-processed and masked map.
Sample
  • Complex: Nup98(298-327)
    • Protein or peptide: Nuclear pore complex protein Nup98Nuclear pore
KeywordsNup98 / 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 / 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 ...telomere tethering at nuclear periphery / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / 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 / RNA export from nucleus / positive regulation of mRNA splicing, via spliceosome / 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 / tRNA processing in the nucleus / 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 / RHO GTPases Activate Formins / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / 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 autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like
Similarity search - Domain/homology
Nuclear pore complex protein Nup98-Nup96
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsIbanez de Opakua A / Cima-Omori S / Dienemann C / Zweckstetter M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)787679European Union
CitationJournal: To Be Published
Title: Structural insights into specific FG nucleoporin repeats for Nup98 hydrogel formation
Authors: Ibanez de Opakua A / Cima-Omori S / Dienemann C / Zweckstetter M
History
DepositionFeb 9, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16671.png

Downloads & links

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Map

FileDownload / File: emd_16671.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed and masked map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 224 pix.
= 235.2 Å		1.05 Å/pix.
x 224 pix.
= 235.2 Å		1.05 Å/pix.
x 224 pix.
= 235.2 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: 0.04
Minimum - Maximum-0.12754135 - 0.2974759
Average (Standard dev.)0.0002705501 (±0.005737142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 235.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Relion refinement half map 2.

Fileemd_16671_half_map_1.map
AnnotationRelion refinement half map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Relion refinement half map 1.

Fileemd_16671_half_map_2.map
AnnotationRelion refinement 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 : Nup98(298-327)

EntireName: Nup98(298-327)
Components
  • Complex: Nup98(298-327)
    • Protein or peptide: Nuclear pore complex protein Nup98Nuclear pore

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Supramolecule #1: Nup98(298-327)

SupramoleculeName: 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)

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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: 25 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.034271 KDa
SequenceString:
TGFSFGNTST IGQPSTNTMG LFGVTQASQP

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: 6.5 / Details: In water.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 recordingFilm 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

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Image processing

Startup modelType of model: OTHER / Details: Cylinder
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.71 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.19 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Software - details: Final reconstruction software / Number images used: 38099
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: Coot
Output model

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

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