9DDT | pdb_00009ddt

AAGAB pseudoGTPase domain in complex with AP-1 clathrin adaptor complex sigma 3 subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.211 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha- and gamma-adaptin-binding protein p34177Homo sapiensMutation(s): 0 
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AP-1 complex subunit sigma-3154Homo sapiensMutation(s): 0 
Gene Names: AP1S3
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PC3 (Homo sapiens)
Explore Q96PC3 
Go to UniProtKB:  Q96PC3
PHAROS:  Q96PC3
GTEx:  ENSG00000152056 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96PC3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.211 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.294α = 90
b = 61.608β = 90
c = 92.854γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

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 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