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- EMDB-63181: Cryo-EM map of C1ql1-gC1q hexamer and BAI3-eCUB complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63181
TitleCryo-EM map of C1ql1-gC1q hexamer and BAI3-eCUB complex
Map data
Sample
  • Complex: C1ql1-gC1q and BAI3-eCUB complex
    • Complex: BAI3-eCUB
      • Protein or peptide: Adhesion G protein-coupled receptor B3
    • Protein or peptide: C1q-related factor
  • Ligand: CALCIUM ION
KeywordsC1ql1 / BAI3 / synapse / CF-PC / Calcium / SIGNALING 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsLiao L / Niu F / Wei Z
Funding support China, 2 items
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, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63181.png

Downloads & links

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Map

FileDownload / File: emd_63181.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.432 Å		1.07 Å/pix.
x 256 pix.
= 274.432 Å		1.07 Å/pix.
x 256 pix.
= 274.432 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017037974 - 2.028608
Average (Standard dev.)0.0010128738 (±0.021852281)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.432 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63181_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63181_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : C1ql1-gC1q and BAI3-eCUB complex

EntireName: C1ql1-gC1q and BAI3-eCUB complex
Components
  • Complex: C1ql1-gC1q and BAI3-eCUB complex
    • Complex: BAI3-eCUB
      • Protein or peptide: Adhesion G protein-coupled receptor B3
    • Protein or peptide: C1q-related factor
  • Ligand: CALCIUM ION

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Supramolecule #1: C1ql1-gC1q and BAI3-eCUB complex

SupramoleculeName: C1ql1-gC1q and BAI3-eCUB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: BAI3-eCUB

SupramoleculeName: BAI3-eCUB / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: C1q-related factor

MacromoleculeName: C1q-related factor / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 15.184653 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPGSEFTTVP RVAFYAGLKN PHEGYEVLKF DDVVTNLGNN YDAASGKFTC NIPGTYFFTY HVLMRGGDGT SMWADLCKNG QVRASAIAQ DADQNYDYAS NSVILHLDAG DEVFIKLDGG KAHGGNSNKY STFSGFIIYS D

UniProtKB: C1q-related factor

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Macromolecule #2: Adhesion G protein-coupled receptor B3

MacromoleculeName: Adhesion G protein-coupled receptor B3 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.531328 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: AGSAQDFWCS TLVKGVIYGS YSVSEMFPKN FTNCTWTLEN PDPTKYSIYL KFSKKDLSCS NFSLLAYQFD HFSHEKIKDL LRKNHSIMQ LCNSKNAFVF LQYDKNFIQI RRVFPTNFPG LQKKGEEDQK SFFEFLVLNK VSPSQFGCHV LCTWLESCLK S ENGRTESC ...String:
AGSAQDFWCS TLVKGVIYGS YSVSEMFPKN FTNCTWTLEN PDPTKYSIYL KFSKKDLSCS NFSLLAYQFD HFSHEKIKDL LRKNHSIMQ LCNSKNAFVF LQYDKNFIQI RRVFPTNFPG LQKKGEEDQK SFFEFLVLNK VSPSQFGCHV LCTWLESCLK S ENGRTESC GIMYTKCTCP QHLGEWGIDD QSLILLNNVV LPLNEQTEGC LTQELQTTQV CNLTREAKRP PKEEENLYFQ

UniProtKB: Adhesion G protein-coupled receptor B3

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.5 / Details: 50mM Tris, 150mM NaCl, and 10mM CaCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8710226
CTF correctionSoftware - Name: CTFFIND (ver. v4.0) / Type: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.1) / Number images used: 143870
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v4.1)

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Atomic model buiding 1

Initial model
PDB IDChain

4qq2

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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