4IFQ

Crystal structure of Saccharomyces cerevisiae NUP192, residues 2 to 960 [ScNup192(2-960)]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex.

Sampathkumar, P.Kim, S.J.Upla, P.Rice, W.J.Phillips, J.Timney, B.L.Pieper, U.Bonanno, J.B.Fernandez-Martinez, J.Hakhverdyan, Z.Ketaren, N.E.Matsui, T.Weiss, T.M.Stokes, D.L.Sauder, J.M.Burley, S.K.Sali, A.Rout, M.P.Almo, S.C.

(2013) Structure 21: 560-571

  • DOI: 10.1016/j.str.2013.02.005
  • Primary Citation of Related Structures:  
    4IFQ

  • PubMed Abstract: 
  • The nuclear pore complex, composed of proteins termed nucleoporins (Nups), is responsible for nucleocytoplasmic transport in eukaryotes. Nuclear pore complexes (NPCs) form an annular structure composed of the nuclear ring, cytoplasmic ring, a membrane ring, and two inner rings ...

    The nuclear pore complex, composed of proteins termed nucleoporins (Nups), is responsible for nucleocytoplasmic transport in eukaryotes. Nuclear pore complexes (NPCs) form an annular structure composed of the nuclear ring, cytoplasmic ring, a membrane ring, and two inner rings. Nup192 is a major component of the NPC's inner ring. We report the crystal structure of Saccharomyces cerevisiae Nup192 residues 2-960 [ScNup192(2-960)], which adopts an α-helical fold with three domains (i.e., D1, D2, and D3). Small angle X-ray scattering and electron microscopy (EM) studies reveal that ScNup192(2-960) could undergo long-range transition between "open" and "closed" conformations. We obtained a structural model of full-length ScNup192 based on EM, the structure of ScNup192(2-960), and homology modeling. Evolutionary analyses using the ScNup192(2-960) structure suggest that NPCs and vesicle-coating complexes are descended from a common membrane-coating ancestral complex. We show that suppression of Nup192 expression leads to compromised nuclear transport and hypothesize a role for Nup192 in modulating the permeability of the NPC central channel.


    Organizational Affiliation

    Department of Biochemistry, Ullmann Building, Room 409, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP192A970Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: J1216NUP192YJL039C
UniProt
Find proteins for P47054 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47054 
Go to UniProtKB:  P47054
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47054
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.6α = 90
b = 134.6β = 90
c = 234.794γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Structure summary
  • Version 1.2: 2013-03-27
    Changes: Database references
  • Version 1.3: 2013-05-22
    Changes: Database references
  • Version 1.4: 2021-02-10
    Changes: Database references, Derived calculations