Yeast Glo3 GAP domain

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


The Glo3 GAP crystal structure supports the molecular niche model for ArfGAPs in COPI coats.

Xie, B.Jung, C.Chandra, M.Engel, A.Kendall, A.K.Jackson, L.P.

(2021) Adv Biol Regul 79: 100781-100781

  • DOI: https://doi.org/10.1016/j.jbior.2020.100781
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Arf GTPase activating (ArfGAP) proteins are critical regulatory and effector proteins in membrane trafficking pathways. Budding yeast contain two ArfGAP proteins (Gcs1 and Glo3) implicated in COPI coat function at the Golgi, and yeast require Glo3 catalytic function for viability. A new X-ray crystal structure of the Glo3 GAP domain was determined at 2.1 Å resolution using molecular replacement methods. The structure reveals a Cys 4 -family zinc finger motif with an invariant residue (R59) positioned to act as an "arginine finger" during catalysis. Comparisons among eukaryotic GAP domains show a key difference between ArfGAP1 and ArfGAP2/3 family members in the final helix located within the domain. Conservation at both the sequence and structural levels suggest the Glo3 GAP domain interacts with yeast Arf1 switch I and II regions to promote catalysis. Together, the structural data presented here provide additional evidence for placing Glo3 near Arf1 triads within membrane-assembled COPI coats and further support the molecular niche model for COPI coat regulation by ArfGAPs.

  • Organizational Affiliation

    Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylation factor GTPase-activating protein GLO3A [auth B],
B [auth A],
157Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GLO3YER122C
Find proteins for P38682 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38682 
Go to UniProtKB:  P38682
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38682
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.369α = 90
b = 74.031β = 105.344
c = 77.902γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM119525

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description