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: 4.1 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.319 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/nsmb.2998

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fusion Protein of Sec13 and Nup145C
A
876Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799)N/A
Find proteins for G2QES5 (Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Go to UniProtKB:  G2QES5
Find proteins for G2QEZ2 (Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Go to UniProtKB:  G2QEZ2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nup85
B
933Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799)N/A
Find proteins for G2Q7J4 (Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Go to UniProtKB:  G2Q7J4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nup120
C
313Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799)N/A
Find proteins for G2Q2S2 (Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Go to UniProtKB:  G2Q2S2
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.319 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/175 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 104.984α = 90.00
b = 212.022β = 107.21
c = 170.643γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM077537

Revision History 

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-04-22
    Type: Database references
  • Version 1.2: 2015-05-27
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Source and taxonomy