9LKK | pdb_00009lkk

Crystal structure of C1ql1-gC1q hexamer


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
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wwPDB Validation   3D Report Full Report


This is version 1.0 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 

  • DOI: https://doi.org/10.1038/s41467-025-66254-1
  • Primary Citation of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C1q-related factor
A, B, C, D, E
A, B, C, D, E, F, G, H, I
140Mus musculusMutation(s): 0 
Gene Names: C1ql1C1qrfCrfCtrp14
UniProt
Find proteins for O88992 (Mus musculus)
Explore O88992 
Go to UniProtKB:  O88992
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO88992
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC

Download Ideal Coordinates CCD File 
AA [auth C],
O [auth A],
T [auth B]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
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
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
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
CL
Query on CL

Download Ideal Coordinates CCD File 
OA [auth F],
RA [auth G],
UA [auth I],
Z [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • 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) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.367α = 90
b = 110.634β = 90
c = 114.921γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32471250
National Natural Science Foundation of China (NSFC)China32471262

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release