6X03

Nup84-Nup133 (aa521-1157) from S. cerevisiae bound by VHH-SAN8 and VHH-SAN9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.30 Å
  • R-Value Free: 0.353 
  • R-Value Work: 0.335 
  • R-Value Observed: 0.337 

Starting Model: other
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif.

Nordeen, S.A.Turman, D.L.Schwartz, T.U.

(2020) Nat Commun 11: 6060-6060

  • DOI: https://doi.org/10.1038/s41467-020-19885-5
  • Primary Citation of Related Structures:  
    6X02, 6X03, 6X04, 6X05

  • PubMed Abstract: 

    The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions. Transport into and out of the nucleus occurs through the nuclear pore complex (NPC). The heptameric Nup84 or Y complex is an essential scaffolding component of the NPC. Here we report two nanobody-bound structures: the full-length Nup84-Nup133 C-terminal domain complex and the Nup133 N-terminal domain, both from S. cerevisiae. Together with previously published structures, this work enables the structural description of the entire 575 kDa Y complex from one species. The structure of Nup84-Nup133 CTD details the high flexibility of this dimeric unit of the Y complex. Further, the Nup133 NTD contains a structurally conserved amphipathic lipid packing sensor motif, confirmed by liposome interaction studies. The presented structures reveal important details about the function of the Y complex that affect our understanding of NPC structure and assembly.


  • Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP84726Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUP84YDL116W
UniProt
Find proteins for P52891 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P52891 
Go to UniProtKB:  P52891
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52891
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP133643Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUP133RAT3YKR082WYKR402
UniProt
Find proteins for P36161 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36161 
Go to UniProtKB:  P36161
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UniProt GroupP36161
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VHH-SAN8131Vicugna pacosMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
VHH-SAN9128Vicugna pacosMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.30 Å
  • R-Value Free: 0.353 
  • R-Value Work: 0.335 
  • R-Value Observed: 0.337 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.252α = 90
b = 295.205β = 90
c = 295.609γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM077537

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references, Other
  • Version 1.2: 2024-04-03
    Changes: Refinement description