Crystal structure of the xNup93-Nb2t VHH antibody

Experimental Data Snapshot

  • Resolution: 1.41 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


A checkpoint function for Nup98 in nuclear pore formation suggested by novel inhibitory nanobodies.

Sola Colom, M.Fu, Z.Gunkel, P.Guttler, T.Trakhanov, S.Srinivasan, V.Gregor, K.Pleiner, T.Gorlich, D.

(2024) EMBO J 43: 2198-2232

  • DOI: https://doi.org/10.1038/s44318-024-00081-w
  • Primary Citation of Related Structures:  
    7NOW, 7NQA, 7ZOX, 8CDS, 8CDT, 8OZB

  • PubMed Abstract: 

    Nuclear pore complex (NPC) biogenesis is a still enigmatic example of protein self-assembly. We now introduce several cross-reacting anti-Nup nanobodies for imaging intact nuclear pore complexes from frog to human. We also report a simplified assay that directly tracks postmitotic NPC assembly with added fluorophore-labeled anti-Nup nanobodies. During interphase, NPCs are inserted into a pre-existing nuclear envelope. Monitoring this process is challenging because newly assembled NPCs are indistinguishable from pre-existing ones. We overcame this problem by inserting Xenopus-derived NPCs into human nuclear envelopes and using frog-specific anti-Nup nanobodies for detection. We further asked whether anti-Nup nanobodies could serve as NPC assembly inhibitors. Using a selection strategy against conserved epitopes, we obtained anti-Nup93, Nup98, and Nup155 nanobodies that block Nup-Nup interfaces and arrest NPC assembly. We solved structures of nanobody-target complexes and identified roles for the Nup93 α-solenoid domain in recruiting Nup358 and the Nup214·88·62 complex, as well as for Nup155 and the Nup98 autoproteolytic domain in NPC scaffold assembly. The latter suggests a checkpoint linking pore formation to the assembly of the Nup98-dominated permeability barrier.

  • Organizational Affiliation

    Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
15-Nup93 tracking VHH antibody123Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.41 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.968α = 90
b = 99.968β = 90
c = 30.707γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
Boehringer Ingelheim Fonds (BIF)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references
  • Version 1.2: 2024-06-12
    Changes: Database references