Crystal structure of SmgGDS-558

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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This is version 1.2 of the entry. See complete history


Structure-based analysis of the guanine nucleotide exchange factor SmgGDS reveals armadillo-repeat motifs and key regions for activity and GTPase binding

Shimizu, H.Toma-Fukai, S.Saijo, S.Shimizu, N.Kontani, K.Katada, T.Shimizu, T.

(2017) J Biol Chem 292: 13441-13448

  • DOI: https://doi.org/10.1074/jbc.M117.792556
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Small GTPases are molecular switches that have critical biological roles and are controlled by GTPase-activating proteins and guanine nucleotide exchange factors (GEFs). The smg GDP dissociation stimulator (SmgGDS) protein functions as a GEF for the RhoA and RhoC small GTPases. SmgGDS has various regulatory roles, including small GTPase trafficking and localization and as a molecular chaperone, and interacts with many small GTPases possessing polybasic regions. Two SmgGDS splice variants, SmgGDS-558 and SmgGDS-607, differ in GEF activity and binding affinity for RhoA depending on the lipidation state, but the reasons for these differences are unclear. Here we determined the crystal structure of SmgGDS-558, revealing a fold containing tandem copies of armadillo repeats not present in other GEFs. We also observed that SmgGDS harbors distinct positively and negatively charged regions, both of which play critical roles in binding to RhoA and GEF activity. This is the first report demonstrating a relationship between the molecular function and atomic structure of SmgGDS. Our findings indicate that the two SmgGDS isoforms differ in GTPase binding and GEF activity, depending on the lipidation state, thus providing useful information about the cellular functions of SmgGDS in cells.

  • Organizational Affiliation

    the Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan, and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rap1 GTPase-GDP dissociation stimulator 1503Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P52306 (Homo sapiens)
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Go to UniProtKB:  P52306
PHAROS:  P52306
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52306
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.33α = 90
b = 51.115β = 92.77
c = 52.444γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Database references