8CI8

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

• PDB DOI: https://doi.org/10.2210/pdb8CI8/pdb
• EM Map EMD-16671: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2023-02-09 Released: 2024-02-21 
• Deposition Author(s): Ibanez de Opakua, A., Cima-Omori, S., Dienemann, C., Zweckstetter, M.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.67 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Structural insights into specific FG nucleoporin repeats for Nup98 hydrogel formation

Ibanez de Opakua, A., Cima-Omori, S., Dienemann, C., Zweckstetter, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 25-mer - A15B5C5 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 25-mer - A5B5C5D1E1F1G1H1I1J1K1L1M1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 75.86 kDa 
• Atom Count: 3,430 
• Modelled Residue Count: 485 
• Deposited Residue Count: 750 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup98	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y	30	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P52948 (Homo sapiens) Explore P52948  Go to UniProtKB:  P52948
PHAROS:  P52948 GTEx:  ENSG00000110713

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.67 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): Ibanez de Opakua, A., Cima-Omori, S., Dienemann, C., Zweckstetter, M.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	787679

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release