3HXR

Nucleoporin Nup120 from S.cerevisiae (aa 1-757)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of the scaffold nucleoporin Nup120 reveals a new and unexpected domain architecture.

Leksa, N.C.Brohawn, S.G.Schwartz, T.U.

(2009) Structure 17: 1082-1091

  • DOI: 10.1016/j.str.2009.06.003

  • PubMed Abstract: 
  • Nucleocytoplasmic transport is mediated by nuclear pore complexes (NPCs), enormous protein assemblies residing in circular openings in the nuclear envelope. The NPC is modular, with transient and stable components. The stable core is essentially buil ...

    Nucleocytoplasmic transport is mediated by nuclear pore complexes (NPCs), enormous protein assemblies residing in circular openings in the nuclear envelope. The NPC is modular, with transient and stable components. The stable core is essentially built from two multiprotein complexes, the Y-shaped heptameric Nup84 complex and the Nic96 complex, arranged around an eightfold axis. We present the crystal structure of Nup120(1-757), one of the two short arms of the Y-shaped Nup84 complex. The protein adopts a compact oval shape built around a novel bipartite alpha-helical domain intimately integrated with a beta-propeller domain. The domain arrangement is substantially different from the Nup85*Seh1 complex, which forms the other short arm of the Y. With the data presented here, we establish that all three branches of the Y-shaped Nup84 complex are tightly connected by helical interactions and that the beta-propellers likely form interaction site(s) to neighboring complexes.


    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NUP120
A
761Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: NUP120 (RAT2)
Find proteins for P35729 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P35729
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 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.244 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 114.600α = 90.00
b = 153.690β = 90.00
c = 52.980γ = 90.00
Software Package:
Software NamePurpose
SHELXEmodel building
HKL-2000data collection
SHELXCDphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description