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- PDB-9lkl: Cryo-EM map of C1ql1-gC1q hexamer and BAI3-eCUB complex -

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Basic information

Entry
Database: PDB / ID: 9lkl
TitleCryo-EM map of C1ql1-gC1q hexamer and BAI3-eCUB complex
Components
  • Adhesion G protein-coupled receptor B3
  • C1q-related factor
KeywordsSIGNALING PROTEIN / C1ql1 / BAI3 / synapse / CF-PC / Calcium
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 / regulation of synapse maturation / myoblast fusion / positive regulation of synapse assembly / regulation of dendrite morphogenesis ...climbing fiber / motor learning / cerebellar climbing fiber to Purkinje cell synapse / maintenance of synapse structure / regulation of synapse pruning / collagen trimer / regulation of synapse maturation / myoblast fusion / positive regulation of synapse assembly / regulation of dendrite morphogenesis / neuron remodeling / synaptic cleft / GTPase activator activity / negative regulation of angiogenesis / postsynaptic density membrane / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / presynapse / cell surface receptor signaling pathway / postsynapse / G protein-coupled receptor signaling pathway / signaling receptor binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
GPCR, family 2, brain-specific angiogenesis inhibitor / Adhesion G protein-coupled receptor B, N-terminal domain / Adhesion GPCR B N-terminal region / : / GAIN domain, N-terminal / AGRL2-4 GAIN subdomain A / C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. ...GPCR, family 2, brain-specific angiogenesis inhibitor / Adhesion G protein-coupled receptor B, N-terminal domain / Adhesion GPCR B N-terminal region / : / GAIN domain, N-terminal / AGRL2-4 GAIN subdomain A / C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / : / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / Tumour necrosis factor-like domain superfamily / CUB domain / CUB domain profile. / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2.
Similarity search - Domain/homology
Adhesion G protein-coupled receptor B3 / C1q-related factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 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 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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: Adhesion G protein-coupled receptor B3
E: Adhesion G protein-coupled receptor B3
F: C1q-related factor
G: C1q-related factor
H: C1q-related factor
I: Adhesion G protein-coupled receptor B3
J: Adhesion G protein-coupled receptor B3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,55418
Polymers201,23310
Non-polymers3218
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#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.: 6
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
#2: Protein
Adhesion G protein-coupled receptor B3 / Brain-specific angiogenesis inhibitor 3


Mass: 27531.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADGRB3, BAI3, KIAA0550 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O60242
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1C1ql1-gC1q and BAI3-eCUB complexCOMPLEX#1-#20RECOMBINANT
2BAI3-eCUBCOMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mus musculus (house mouse)10090
32Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli BL21(DE3) (bacteria)469008
32Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.5 / Details: 50mM Tris, 150mM NaCl, and 10mM CaCl2
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2SerialEMv3.7image acquisition
4CTFFINDv4.0CTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCv4.1initial Euler assignment
10cryoSPARCv4.1final Euler assignment
11cryoSPARCv4.1classification
12cryoSPARCv4.13D reconstruction
13PHENIX1.19.2_4158model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 8710226
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143870 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
14qq2

4qq2

14qq21PDBexperimental model
21AlphaFoldin silico model
RefinementHighest resolution: 3.48 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311477
ELECTRON MICROSCOPYf_angle_d0.70715506
ELECTRON MICROSCOPYf_dihedral_angle_d4.0741511
ELECTRON MICROSCOPYf_chiral_restr0.0471634
ELECTRON MICROSCOPYf_plane_restr0.0051991

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