5C3L

Structure of the metazoan Nup62.Nup58.Nup54 nucleoporin complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.266 

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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
  • Primary Citation of Related Structures:  
    5C2U, 5C3L

  • 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. 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nup54A333Xenopus laevisMutation(s): 0 
Gene Names: nup54.Snup54XELAEV_18009519mg
UniProt
Find proteins for K9ZTJ6 (Xenopus laevis)
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin Nup58B142Xenopus laevisMutation(s): 0 
Gene Names: MGC84997nup58.Snup58XELAEV_18016222mg
UniProt
Find proteins for Q5EAX5 (Xenopus laevis)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin Nup62C150Xenopus laevisMutation(s): 0 
Gene Names: nup62IL4I1nup62.LXELAEV_18038559mg
UniProt
Find proteins for Q91349 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody Nb15D119Camelus dromedariusMutation(s): 0 
Gene Names: Immunoglobulin G
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Part of Nup54 N-terminus with weak electron density, built as poly-alanine.E [auth H]14Xenopus laevisMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.266 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.57α = 90
b = 167.57β = 90
c = 142.72γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-26
    Type: Initial release