9W5C | pdb_00009w5c

Complex structure of MAGI3 WW1 and IQSEC3 PPxY motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.218 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9W5C

This is version 1.1 of the entry. See complete history

Literature

Extended motif recognition tunes WW domain affinity in MAGI-IQSEC complexes.

Wang, J.Li, Y.Wu, Y.Lin, L.Zhu, J.

(2026) FEBS J 

  • DOI: https://doi.org/10.1111/febs.70509
  • Primary Citation Related Structures: 
    9W5C

  • PubMed Abstract: 

    Many proteins containing WW domains interact with proline-rich PPxY motifs, raising questions regarding how they achieve specificity in cellular contexts. Here, we characterize the WW domain-mediated interactions between the MAGI and IQSEC protein families, which play critical roles in neurodevelopment and synaptic signaling. The high-resolution crystal structure of the MAGI3-IQSEC3 complex reveals that an extended sequence C terminus to the canonical PPxY motif in IQSEC3 engages a previously uncharacterized binding site on the WW1 domain of MAGI3. This extension interface enhances binding affinity by dozens-fold, and mutagenesis of key residues within this site abrogates complex formation, demonstrating its functional necessity. This bipartite recognition mode is evolutionarily conserved across MAGI and IQSEC family members. Our work elucidates the structural basis governing MAGI-IQSEC assembly and establishes a generalizable model whereby motif extensions enable high-affinity, specific target selection by WW domains, with broad implications for modular domain-mediated signaling networks.


  • Organizational Affiliation
    • Bio-X Institutes, MOE Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, China.

Macromolecule Content 

  • Total Structure Weight: 43.39 kDa 
  • Atom Count: 2,656 
  • Modeled Residue Count: 303 
  • Deposited Residue Count: 372 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3
A, C, E, G, I
A, C, E, G, I, K
44Rattus norvegicusMutation(s): 0 
Gene Names: Magi3Slipr
UniProt
Find proteins for Q9JK71 (Rattus norvegicus)
Explore Q9JK71 
Go to UniProtKB:  Q9JK71
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JK71
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
IQ motif and SEC7 domain-containing protein 3
B, D, F, H, J
B, D, F, H, J, L
18Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q3TES0 (Mus musculus)
Explore Q3TES0 
Go to UniProtKB:  Q3TES0
IMPC:  MGI:2677208
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3TES0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.472α = 90
b = 78.971β = 93.52
c = 48.78γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-25
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Database references