Cryo-em structure of the Nup98 fibril polymorph 3

Experimental Data Snapshot

  • Resolution: 2.79 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report

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Molecular interactions of FG nucleoporin repeats at high resolution.

Ibanez de Opakua, A.Geraets, J.A.Frieg, B.Dienemann, C.Savastano, A.Rankovic, M.Cima-Omori, M.S.Schroder, G.F.Zweckstetter, M.

(2022) Nat Chem 14: 1278-1285

  • DOI: https://doi.org/10.1038/s41557-022-01035-7
  • Primary Citation of Related Structures:  
    7Q64, 7Q65, 7Q66, 7Q67

  • PubMed 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 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.

  • Organizational Affiliation

    German Center for Neurodegenerative Diseases, Göttingen, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup98
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
40Homo sapiensMutation(s): 0 
Gene Names: NUP98ADAR2
UniProt & NIH Common Fund Data Resources
Find proteins for P52948 (Homo sapiens)
Explore P52948 
Go to UniProtKB:  P52948
PHAROS:  P52948
GTEx:  ENSG00000110713 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52948
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.79 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)Germany787679
German Research Foundation (DFG)Germany656281

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references