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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • 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 membran ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NUP192
A
970Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NUP192
Find proteins for P47054 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P47054
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 134.600α = 90.00
b = 134.600β = 90.00
c = 234.794γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHENIXphasing
SCALEPACKdata scaling
CBASSdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-02-27
    Type: Structure summary
  • Version 1.2: 2013-03-27
    Type: Database references
  • Version 1.3: 2013-05-22
    Type: Database references