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- PDB-9lkk: Crystal structure of C1ql1-gC1q hexamer -

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Basic information

Entry
Database: PDB / ID: 9lkk
TitleCrystal structure of C1ql1-gC1q hexamer
ComponentsC1q-related factor
KeywordsSIGNALING PROTEIN / C1ql1 / synapse / CF-PC / Calcium / secreted protein
Function / homology
Function and homology information


climbing fiber / motor learning / cerebellar climbing fiber to Purkinje cell synapse / maintenance of synapse structure / regulation of synapse pruning / collagen trimer / neuron remodeling / synaptic cleft / presynapse / signaling receptor binding / cytoplasm
Similarity search - Function
: / C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies)
Similarity search - Domain/homology
CACODYLATE ION / C1q-related factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsLiao, L. / Niu, F. / Wei, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32471250 China
National Natural Science Foundation of China (NSFC)32471262 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of calcium-dependent C1ql1/BAI3 assemblies in synaptic connectivity.
Authors: Liangyu Liao / Ying Han / Fengfeng Niu / Yingjie Wang / Yang Lu / Shun Xu / Houming Zhu / Leishu Lin / Jinman Xiao / Hoi In Tou / Jiali Gao / Bo Zhang / Zhiyi Wei /
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 ...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.
History
DepositionJan 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C1q-related factor
B: C1q-related factor
C: C1q-related factor
D: C1q-related factor
E: C1q-related factor
F: C1q-related factor
G: C1q-related factor
H: C1q-related factor
I: C1q-related factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,87347
Polymers136,6629
Non-polymers2,21138
Water8,953497
1
A: C1q-related factor
B: C1q-related factor
C: C1q-related factor
G: C1q-related factor
H: C1q-related factor
I: C1q-related factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,45130
Polymers91,1086
Non-polymers1,34324
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22110 Å2
ΔGint-248 kcal/mol
Surface area24870 Å2
MethodPISA
2
D: C1q-related factor
E: C1q-related factor
F: C1q-related factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,42317
Polymers45,5543
Non-polymers86914
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-68 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.367, 110.634, 114.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 9 molecules ABCDEFGHI

#1: Protein
C1q-related factor / C1q and tumor necrosis factor-related protein 14 / C1q/TNF-related protein 14 / CTRP14 / Complement ...C1q and tumor necrosis factor-related protein 14 / C1q/TNF-related protein 14 / CTRP14 / Complement component 1 Q subcomponent-like 1


Mass: 15184.653 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: C1ql1, C1qrf, Crf, Ctrp14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O88992

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Non-polymers , 5 types, 535 molecules

#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: protein solution: 50 mM Tris, pH 7.5, 500 mM NaCl; crystal solution: 0.1 M Na Cacodylate, pH 6.0, 25% MPD, and 0.05 M Ca acetate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.22→57.46 Å / Num. obs: 70092 / % possible obs: 99.95 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 14.48
Reflection shellResolution: 2.22→2.3 Å / Num. unique obs: 6923 / CC1/2: 0.725 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→57.46 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 3340 4.77 %
Rwork0.1718 --
obs0.1737 70091 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→57.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9084 0 27 497 9608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079400
X-RAY DIFFRACTIONf_angle_d0.88912716
X-RAY DIFFRACTIONf_dihedral_angle_d7.2861304
X-RAY DIFFRACTIONf_chiral_restr0.0561318
X-RAY DIFFRACTIONf_plane_restr0.0051676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.250.31691460.2642747X-RAY DIFFRACTION100
2.25-2.290.2751690.24052663X-RAY DIFFRACTION100
2.29-2.320.2521610.22082733X-RAY DIFFRACTION100
2.32-2.360.23091310.21462779X-RAY DIFFRACTION100
2.36-2.40.23781100.21372784X-RAY DIFFRACTION100
2.4-2.440.30641170.2062765X-RAY DIFFRACTION100
2.44-2.490.27091320.19572759X-RAY DIFFRACTION100
2.49-2.540.22531260.19372758X-RAY DIFFRACTION100
2.54-2.60.26271470.18442744X-RAY DIFFRACTION100
2.6-2.660.25771430.19132785X-RAY DIFFRACTION100
2.66-2.720.27911180.18772754X-RAY DIFFRACTION100
2.72-2.80.25961270.182775X-RAY DIFFRACTION100
2.8-2.880.20721100.17492779X-RAY DIFFRACTION100
2.88-2.970.20661090.16592813X-RAY DIFFRACTION100
2.97-3.080.19311170.16762799X-RAY DIFFRACTION100
3.08-3.20.20451200.16182798X-RAY DIFFRACTION100
3.2-3.350.20531340.1582792X-RAY DIFFRACTION100
3.35-3.520.17371720.14892731X-RAY DIFFRACTION100
3.52-3.740.19811880.14732749X-RAY DIFFRACTION100
3.74-4.030.19711490.14622787X-RAY DIFFRACTION100
4.03-4.440.15721720.13842803X-RAY DIFFRACTION100
4.44-5.080.15731700.1392789X-RAY DIFFRACTION100
5.08-6.40.24981370.19032880X-RAY DIFFRACTION100
6.4-57.460.26841350.21342985X-RAY DIFFRACTION99

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