9DDS | pdb_00009dds

Crystal structure of human AAGAB G domain with E144K mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.213 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural basis of pseudoGTPase-mediated protein-protein interactions.

Wang, B.Yang, R.Wan, C.Tian, Y.Wu, J.Adewole, T.S.Roy, S.Li, S.Shen, J.Yin, Q.

(2025) Structure 33: 1676-1687.e5

  • DOI: https://doi.org/10.1016/j.str.2025.07.009
  • Primary Citation Related Structures: 
    9DDS, 9DDT

  • PubMed Abstract: 

    GTPases regulate cellular processes through conformational changes triggered by guanine nucleotide binding. Recently, pseudoGTPases, the catalytically inactive counterparts of GTPases, have been identified across species from bacteria to human, although their functions and mechanisms remain unexplored. Here, we demonstrate that the N-terminal region of the assembly chaperone AAGAB is a class I pseudoGTPase using biochemistry and X-ray crystallography. Furthermore, we discovered that the AAGAB pseudoGTPase domain (psGD) interacts with the σ subunits of AP1 and AP2 adaptor complexes, which are heterotetrameric complexes involved in clathrin-mediated membrane trafficking. AAGAB psGD engages the σ subunits via a unique interface distinct from the conventional GTPase interacting regions. Further biochemical and cell-based assays confirmed the crucial role of the newly identified interface in binding and membrane trafficking. Collectively, our results establish AAGAB pseudoGTPase domain as a critical protein-protein interaction module. These findings offer new insight into the structural basis and molecular mechanisms of pseudoGTPases.


  • Organizational Affiliation
    • Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.

Macromolecule Content 

  • Total Structure Weight: 39.35 kDa 
  • Atom Count: 2,924 
  • Modeled Residue Count: 328 
  • Deposited Residue Count: 354 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha- and gamma-adaptin-binding protein p34
A, B
177Homo sapiensMutation(s): 1 
Gene Names: AAGAB
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PD74 (Homo sapiens)
Explore Q6PD74 
Go to UniProtKB:  Q6PD74
PHAROS:  Q6PD74
GTEx:  ENSG00000103591 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PD74
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.213 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.268α = 90
b = 94.349β = 90
c = 102.796γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM138685

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Database references