5C2U

Ferredoxin-like domain of nucleoporin Nup54 bound to a nanobody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the metazoan Nup62Nup58Nup54 nucleoporin complex.

Chug, H.Trakhanov, S.Hulsmann, B.B.Pleiner, T.Gorlich, D.

(2015) Science 350: 106-110

  • DOI: 10.1126/science.aac7420
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Nuclear pore complexes (NPCs) conduct nucleocytoplasmic transport and gain transport selectivity through nucleoporin FG domains. Here, we report a structural analysis of the FG Nup62•58•54 complex, which is a crucial component of the transport system ...

    Nuclear pore complexes (NPCs) conduct nucleocytoplasmic transport and gain transport selectivity through nucleoporin FG domains. Here, we report a structural analysis of the FG Nup62•58•54 complex, which is a crucial component of the transport system. It comprises a ≈13 nanometer-long trimerization interface with an unusual 2W3F coil, a canonical heterotrimeric coiled coil, and a kink that enforces a compact six-helix bundle. Nup54 also contains a ferredoxin-like domain. We further identified a heterotrimeric Nup93-binding module for NPC anchorage. The quaternary structure alternations in the Nup62 complex, which were previously proposed to trigger a general gating of the NPC, are incompatible with the trimer structure. We suggest that the highly elongated Nup62 complex projects barrier-forming FG repeats far into the central NPC channel, supporting a barrier that guards the entire cross section.


    Organizational Affiliation

    Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. goerlich@mpibpc.mpg.de.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NanobodyB131Camelus dromedariusMutation(s): 0 
Gene Names: Immunoglobulin G
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nup54A143Xenopus laevisMutation(s): 0 
Gene Names: nup54XELAEV_18009519mg
Find proteins for K9ZTJ6 (Xenopus laevis)
Explore K9ZTJ6 
Go to UniProtKB:  K9ZTJ6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.86α = 90
b = 90.86β = 90
c = 57.6γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Database references
  • Version 1.2: 2015-10-14
    Changes: Database references