8YM2 | pdb_00008ym2

Crystal structure of AIDA-1 PTB domain in complex with SynGAP NPxF motif

• PDB DOI: https://doi.org/10.2210/pdb8YM2/pdb

• Classification: PROTEIN BINDING
• Organism(s): Mus musculus, Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-08 Released: 2024-05-29 
• Deposition Author(s): Wang, X., Wang, Y., Cai, Q., Zhang, M.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.264 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

AIDA-1/ANKS1B Binds to the SynGAP Family RasGAPs with High Affinity and Specificity.

Wang, X., Wang, Y., Cai, Q., Zhang, M.

(2024) J Mol Biology 436: 168608-168608

• PubMed: 38759928 
• DOI: https://doi.org/10.1016/j.jmb.2024.168608
• Primary Citation Related Structures: 
  8YM2


• PubMed Abstract: 
  

  AIDA-1, encoded by ANKS1B, is an abundant postsynaptic scaffold protein essential for brain development. Mutations of ANKS1B are closely associated with various psychiatric disorders. However, very little is known regarding the molecular mechanisms underlying AIDA-1's involvements under physiological and pathophysiological conditions. Here, we discovered an interaction between AIDA-1 and the SynGAP family Ras-GTPase activating protein (GAP) via affinity purification using AIDA-1d as the bait. Biochemical studies showed that the PTB domain of AIDA-1 binds to an extended NPx[F/Y]-motif of the SynGAP family proteins with high affinities. The high-resolution crystal structure of AIDA-1 PTB domain in complex with the SynGAP NPxF-motif revealed the molecular mechanism governing the specific interaction between AIDA-1 and SynGAP. Our study not only explains why patients with ANKS1B or SYNGAP1 mutations share overlapping clinical phenotypes, but also allows identification of new AIDA-1 binding targets such as Ras and Rab interactors.

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Organizational Affiliation: 
• Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China. Electronic address: [e-mail].
Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, China.
Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen 518036, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China. Electronic address: [e-mail].

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: light scattering

Macromolecule Content 

• Total Structure Weight: 19.58 kDa 
• Atom Count: 1,295 
• Modeled Residue Count: 158 
• Deposited Residue Count: 173 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ankyrin repeat and sterile alpha motif domain-containing protein 1B	A	162	Mus musculus	Mutation(s): 0  Gene Names: Anks1b
UniProt
Find proteins for Q8BIZ1 (Mus musculus) Explore Q8BIZ1  Go to UniProtKB:  Q8BIZ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras/Rap GTPase-activating protein SynGAP	B	11	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q9QUH6 (Rattus norvegicus) Explore Q9QUH6  Go to UniProtKB:  Q9QUH6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.264 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.919	α = 90
b = 112.919	β = 90
c = 112.919	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Wang, X., Wang, Y., Cai, Q., Zhang, M.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2019YFA0508402

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release
  
• Version 1.1: 2024-06-05
  Changes: Database references