9DDT | pdb_00009ddt

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

• PDB DOI: https://doi.org/10.2210/pdb9DDT/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-28 Released: 2025-07-16 
• Deposition Author(s): Wang, B., Tian, Y., Yin, Q.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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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

Literature

A pseudoGTPase mediates chaperone-substrate interaction in membrane trafficking complex assembly

Wang, B., Tian, Y., Yin, Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: cross-linking

Macromolecule Content 

• Total Structure Weight: 37.98 kDa 
• Atom Count: 2,652 
• Modeled Residue Count: 286 
• Deposited Residue Count: 331 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha- and gamma-adaptin-binding protein p34	A	177	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-1 complex subunit sigma-3	B	154	Homo sapiens	Mutation(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

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 = 50.294	α = 90
b = 61.608	β = 90
c = 92.854	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Wang, B., Tian, Y., Yin, Q.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM138685

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release