Glutamate dehydrogenase from E. coli

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Molecular basis for Nup37 and ELY5/ELYS recruitment to the nuclear pore complex.

Bilokapic, S.Schwartz, T.U.

(2012) Proc Natl Acad Sci U S A 109: 15241-15246

  • DOI: https://doi.org/10.1073/pnas.1205151109
  • Primary Citation of Related Structures:  
    4FCC, 4FHL, 4FHM, 4FHN

  • PubMed Abstract: 

    Nucleocytoplasmic transport is mediated by nuclear pore complexes (NPCs), enormous assemblies composed of multiple copies of ~30 different proteins called nucleoporins. To unravel the basic scaffold underlying the NPC, we have characterized the species-specific scaffold nucleoporin Nup37 and ELY5/ELYS. Both proteins integrate directly via Nup120/160 into the universally conserved heptameric Y-complex, the critical unit for the assembly and functionality of the NPC. We present the crystal structure of Schizosaccharomyces pombe Nup37 in complex with Nup120, a 174-kDa subassembly that forms one of the two short arms of the Y-complex. Nup37 binds near the bend of the L-shaped Nup120 protein, potentially stabilizing the relative orientation of its two domains. By means of reconstitution assays, we pinpoint residues crucial for this interaction. In vivo and in vitro results show that ELY5 binds near an interface of the Nup120-Nup37 complex. Complementary biochemical and cell biological data refine and consolidate the interactions of Nup120 within the current Y-model. Finally, we propose an orientation of the Y-complex relative to the pore membrane, consistent with the lattice model.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
450Escherichia coli O157:H7Mutation(s): 0 
Gene Names: gdhAECs2467Z2793
Find proteins for Q8XDW9 (Escherichia coli O157:H7)
Explore Q8XDW9 
Go to UniProtKB:  Q8XDW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8XDW9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.218α = 90
b = 176.262β = 89.94
c = 150.25γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
ARP/wARPmodel building

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-26
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Structure summary
  • Version 1.2: 2013-01-09
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references