9M46 | pdb_00009m46

Crystal structure of IQSEC2 CC domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.285 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

IQSEC2/BRAG1 may modulate postsynaptic density assembly through Ca2+-induced phase separation.

Bai, G.Huang, R.Nan, X.Zhuang, M.Wu, M.Lian, Y.Cai, Q.Tian, H.Lu, Y.Li, H.Zhang, M.

(2025) J Cell Biol 224

  • DOI: https://doi.org/10.1083/jcb.202503076
  • Primary Citation of Related Structures:  
    9M46

  • PubMed Abstract: 

    IQSEC2, a high-confidence neurodevelopmental disorder risk gene product, is essential for neuronal development and synaptic plasticity. Previous studies established that IQSEC2 dynamically regulates synaptic signaling via Ca2+-dependent release of autoinhibition. In this study, using in vivo mouse models and in vitro biochemistry approaches, we discover that IQSEC2 orchestrates postsynaptic density assembly and dynamics via Ca2+-triggered phase separation. Mechanistically, Ca2+-induced conformational opening leads to phase separation-mediated condensation of IQSEC2 at synapses, a process that requires the N-terminal multimerization domain and intrinsically disordered regions of IQSEC2. We identified a single-point mutation, F367A, in IQSEC2, which exhibits constitutive activity by structurally mimicking the Ca2+-activated state of the WT protein. Mice carrying the Iqsec2_F367A mutation have elevated basal synaptic transmission and impaired activity-dependent plasticity assayed in hippocampal neurons and spatial learning deficits. Thus, IQSEC2 can bidirectionally modulate synaptic strengths via Ca2+-dependent phase separation, and dysregulation of phase separation may be a contributing factor in IQSEC2-related neurodevelopmental disorders.


  • Organizational Affiliation
    • School of Life Sciences, Southern University of Science and Technology , Shenzhen, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IQ motif and SEC7 domain-containing protein 2
A, B, C, D
67Homo sapiensMutation(s): 0 
Gene Names: IQSEC2KIAA0522
UniProt & NIH Common Fund Data Resources
Find proteins for Q5JU85 (Homo sapiens)
Explore Q5JU85 
Go to UniProtKB:  Q5JU85
PHAROS:  Q5JU85
GTEx:  ENSG00000124313 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JU85
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.285 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 20.133α = 90
b = 69.842β = 90
c = 169.327γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
Arcimboldophasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32200773

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Database references