8VWY | pdb_00008vwy

Complex structure of mouse C1ql3 with BAI3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the complex of C1q-like 3 protein with adhesion-GPCR BAI3.

Miao, Y.Wang, H.Jude, K.M.Wang, J.Wang, J.Wernig, M.Sudhof, T.C.

(2025) Commun Biol 8: 693-693

  • DOI: https://doi.org/10.1038/s42003-025-08112-w
  • Primary Citation of Related Structures:  
    8VWY

  • PubMed Abstract: 

    The adhesion-GPCR Brain-specific Angiogenesis Inhibitor-3 (BAI3) plays a crucial role in organizing synapses in the brain. However, how BAI3 engages one of its ligands, the C1q-like proteins (C1qls), remains largely unexplored. Here, we present the single-particle cryo-electron microscopy (cryo-EM) structure of the C1ql3-BAI3 complex at 2.8 Å resolution. The structure reveals a hexameric configuration, where C1ql3 forms a central homotrimer that effectively captures three BAI3 molecules. These BAI3 molecules fit snugly into the grooves between the trimeric C1q domains of the C1qls, employing calcium ion (Ca 2+ )-mediated interactions that differ from previously characterized structures of C1q-like domain-mediated complexes. Furthermore, we conducted mutant analysis and cell surface staining, which confirmed the essential contact residues involved in this interaction. This unique binding mechanism not only enhances our understanding of the C1ql-BAI3-mediated synaptic organization but also sheds light on the functional dynamics of BAI3 in the brain.


  • Organizational Affiliation
    • Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. yimiao@ust.hk.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adhesion G protein-coupled receptor B3A,
E [auth B],
F [auth C]
273Mus musculusMutation(s): 0 
Gene Names: Adgrb3Bai3
UniProt & NIH Common Fund Data Resources
Find proteins for Q80ZF8 (Mus musculus)
Explore Q80ZF8 
Go to UniProtKB:  Q80ZF8
IMPC:  MGI:2441837
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ80ZF8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C1q-like protein 3B [auth E],
C [auth H],
D [auth I]
143Mus musculusMutation(s): 0 
Gene Names: C1ql3C1qlCtrp13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ESN4 (Mus musculus)
Explore Q9ESN4 
Go to UniProtKB:  Q9ESN4
IMPC:  MGI:2387350
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ESN4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Data collection
  • Version 1.2: 2025-08-20
    Changes: Data collection, Database references