9LKK | pdb_00009lkk

Crystal structure of C1ql1-gC1q hexamer

PDB DOI: https://doi.org/10.2210/pdb9LKK/pdb

Classification: SIGNALING PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.210 (Depositor), 0.211 (DCC)
R-Value Work:
0.172 (Depositor), 0.173 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, Shenzhen, Guangdong, China.

Macromolecule Content

Total Structure Weight: 138.87 kDa
Atom Count: 9,706
Modeled Residue Count: 1,170
Deposited Residue Count: 1,260
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C1q-related factor	A, B, C, D, E A, B, C, D, E, F, G, H, I	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O88992
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain O [auth A] SDF format, chain AA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain O [auth A] MOL2 format, chain AA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain O [auth A] mmCIF format, chain AA [auth C]	AA [auth C], O [auth A], T [auth B]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain O [auth A] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain O [auth A] Focus chain T [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain MA [auth E] SDF format, chain U [auth B] SDF format, chain PA [auth F] SDF format, chain LA [auth E] SDF format, chain JA [auth E] SDF format, chain IA [auth D] SDF format, chain HA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain MA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain LA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain IA [auth D] MOL2 format, chain HA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain MA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain LA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain IA [auth D] mmCIF format, chain HA [auth D]	BA [auth C] HA [auth D] IA [auth D] JA [auth E] LA [auth E] BA [auth C], HA [auth D], IA [auth D], JA [auth E], LA [auth E], MA [auth E], PA [auth F], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain PA [auth F] Focus chain U [auth B] Interactions & Density Focus chain BA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain PA [auth F] Focus chain U [auth B]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain L [auth A] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain TA [auth I] SDF format, chain SA [auth H] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain QA [auth G] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain NA [auth F] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain KA [auth E] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain TA [auth I] MOL2 format, chain SA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain NA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain TA [auth I] mmCIF format, chain SA [auth H] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain NA [auth F] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain CA [auth D]	CA [auth D] DA [auth D] EA [auth D] FA [auth D] GA [auth D] CA [auth D], DA [auth D], EA [auth D], FA [auth D], GA [auth D], J [auth A], K [auth A], KA [auth E], L [auth A], M [auth A], N [auth A], NA [auth F], P [auth B], Q [auth B], QA [auth G], R [auth B], S [auth B], SA [auth H], TA [auth I], V [auth C], W [auth C], X [auth C], Y [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth H] Focus chain TA [auth I] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth H] Focus chain TA [auth I] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain UA [auth I] SDF format, chain Z [auth C] SDF format, chain RA [auth G] SDF format, chain OA [auth F] MOL2 format, chain UA [auth I] MOL2 format, chain Z [auth C] MOL2 format, chain RA [auth G] MOL2 format, chain OA [auth F] mmCIF format, chain UA [auth I] mmCIF format, chain Z [auth C] mmCIF format, chain RA [auth G] mmCIF format, chain OA [auth F]	OA [auth F], RA [auth G], UA [auth I], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain OA [auth F] Focus chain RA [auth G] Focus chain UA [auth I] Focus chain Z [auth C] Interactions & Density Focus chain OA [auth F] Focus chain RA [auth G] Focus chain UA [auth I] Focus chain Z [auth C]