4YCZ

Y-COMPLEX HUB (NUP85-NUP120-NUP145C-SEC13 COMPLEX) FROM M. THERMOPHILA (A.K.A. T. HETEROTHALLICA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.319 
  • R-Value Observed: 0.322 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Atomic structure of the Y complex of the nuclear pore.

Kelley, K.Knockenhauer, K.E.Kabachinski, G.Schwartz, T.U.

(2015) Nat Struct Mol Biol 22: 425-431

  • DOI: https://doi.org/10.1038/nsmb.2998
  • Primary Citation of Related Structures:  
    4YCZ

  • PubMed Abstract: 

    The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. Here we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved core of the Y complex has six rather than seven members. Evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.


  • 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
Fusion Protein of Sec13 and Nup145C876Thermothelomyces thermophilus ATCC 42464Mutation(s): 0 
Gene Names: MYCTH_2306744MYCTH_2306912
UniProt
Find proteins for G2QEZ2 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Explore G2QEZ2 
Go to UniProtKB:  G2QEZ2
Find proteins for G2QES5 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Explore G2QES5 
Go to UniProtKB:  G2QES5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsG2QEZ2G2QES5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nup85933Thermothelomyces thermophilus ATCC 42464Mutation(s): 0 
Gene Names: MYCTH_2059413
UniProt
Find proteins for G2Q7J4 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Explore G2Q7J4 
Go to UniProtKB:  G2Q7J4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2Q7J4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nup120313Thermothelomyces thermophilus ATCC 42464Mutation(s): 0 
Gene Names: MYCTH_2296711
UniProt
Find proteins for G2Q2S2 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Explore G2Q2S2 
Go to UniProtKB:  G2Q2S2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2Q2S2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.984α = 90
b = 212.022β = 107.21
c = 170.643γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references
  • Version 1.2: 2015-05-27
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence