9LKM | pdb_00009lkm

Focused map of C1ql1-gC1q trimer and BAI3-eCUB complex

• PDB DOI: https://doi.org/10.2210/pdb9LKM/pdb
• EM Map EMD-63182: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-01-16 Released: 2025-12-17 
• Deposition Author(s): Liao, L., Niu, F., Wei, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.34 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico

Literature

Structural basis of calcium-dependent C1ql1/BAI3 assemblies in synaptic connectivity.

Liao, L., Han, Y., Niu, F., Wang, Y., Lu, Y., Xu, S., Zhu, H., Lin, L., Xiao, J., Tou, H.I., Gao, J., Zhang, B., Wei, Z.

(2025) Nat Commun 16: 11444-11444

• PubMed: 41372137 
• DOI: https://doi.org/10.1038/s41467-025-66254-1
• Primary Citation Related Structures: 
  9LKK, 9LKL, 9LKM


• PubMed Abstract: 
  

  Cell adhesion molecules (CAMs) are pivotal in establishing and maintaining synaptic connectivity. Emerging evidence indicates that some secreted factors within the synaptic cleft, including C1q-like proteins (C1qls), play a crucial role in bridging pre- and post-synapses by connecting the bilateral CAMs. However, the mechanisms of those secreted factors in synapse assembly remain incomplete. Here, we explore C1ql-mediated synaptic connectivity, focusing on the assembly of C1ql1 and its postsynaptic receptor brain-specific angiogenesis inhibitor 3 (BAI3, also called ADGRB3). Our biochemical, structural, and computational analyses reveal that the trimeric globular C1q (gC1q) domain of C1ql1 undergoes a calcium-modulated domain-swapping event to form a hexamer. Cryo-EM study manifests the stabilizing role of calcium ions on the C1ql1_gC1q hexamer in complex with the extended CUB domain of BAI3. Using the gC1q hexamer, full-length C1ql1 further assembles into linear clusters, possibly providing a scaffold to accumulate BAI3 receptors on the plasma membrane. Our cellular and in vivo studies support a role for the gC1q-mediated dynamic assembly of C1ql1 in receptor accumulation and synapse maintenance. Collectively, our findings provide a plausible mechanism of secreted factor-mediated synaptic connectivity, driven by the calcium-modulated assembly of C1qls and their interactions with CAMs.

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Organizational Affiliation: 
• Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, Shenzhen, Guangdong, China.
Department of Neuroscience and Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China.
School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, China.
Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China.
Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China.
Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA.
School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, China. [e-mail].
Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China. [e-mail].
Shenzhen Medical Academy of Research and Translation, Shenzhen, Guangdong, China. [e-mail].
Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, Shenzhen, Guangdong, China. [e-mail].
Department of Neuroscience and Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China. [e-mail].
Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B1C1 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 88.39 kDa 
• Atom Count: 4,445 
• Modeled Residue Count: 569 
• Deposited Residue Count: 798 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C1q-related factor	A, B, C, E [auth H]	140	Mus musculus	Mutation(s): 0  Gene Names: C1ql1, C1qrf, Crf, Ctrp14
UniProt
Find proteins for O88992 (Mus musculus) Explore O88992  Go to UniProtKB:  O88992

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Adhesion G protein-coupled receptor B3	D	238	Homo sapiens	Mutation(s): 0  Gene Names: ADGRB3, BAI3, KIAA0550
UniProt & NIH Common Fund Data Resources
Find proteins for O60242 (Homo sapiens) Explore O60242  Go to UniProtKB:  O60242
PHAROS:  O60242 GTEx:  ENSG00000135298

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	F [auth A], G [auth A], H [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.34 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158
RECONSTRUCTION	cryoSPARC	v4.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Liao, L., Niu, F., Wei, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32471250
National Natural Science Foundation of China (NSFC)	China	32471262

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release
  
• Version 1.1: 2026-01-14
  Changes: Data collection, Database references