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- PDB-8vwy: Complex structure of mouse C1ql3 with BAI3 -

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Basic information

Entry
Database: PDB / ID: 8vwy
TitleComplex structure of mouse C1ql3 with BAI3
Components
  • Adhesion G protein-coupled receptor B3
  • Complement C1q-like protein 3
KeywordsCELL ADHESION / adhesion GPCR / C1q like proteins
Function / homology
Function and homology information


motor learning / postsynaptic density assembly / 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 ...motor learning / postsynaptic density assembly / 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 / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of synapse organization / synaptic cleft / GTPase activator activity / negative regulation of angiogenesis / hippocampal mossy fiber to CA3 synapse / postsynaptic density membrane / G protein-coupled receptor activity / cell surface receptor signaling pathway / postsynapse / glutamatergic synapse / extracellular region / identical protein binding / plasma membrane
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 / Thrombospondin type 1 domain / Collagen triple helix repeat / Thrombospondin type-1 (TSP1) repeat superfamily / Collagen triple helix repeat (20 copies) / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / 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 / Complement C1q-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsMiao, Y. / Sudhof, T.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Commun Biol / Year: 2025
Title: Structure of the complex of C1q-like 3 protein with adhesion-GPCR BAI3.
Authors: Yi Miao / Haoqing Wang / Kevin M Jude / Jie Wang / Jinzhao Wang / Marius Wernig / Thomas C Südhof /
Abstract: The adhesion-GPCR Brain-specific Angiogenesis Inhibitor-3 (BAI3) plays a crucial role in organizing synapses in the brain. However, how BAI3 engages one of its ligands, the C1q-like proteins (C1qls) ...The adhesion-GPCR Brain-specific Angiogenesis Inhibitor-3 (BAI3) plays a crucial role in organizing synapses in the brain. However, how BAI3 engages one of its ligands, the C1q-like proteins (C1qls), remains largely unexplored. Here, we present the single-particle cryo-electron microscopy (cryo-EM) structure of the C1ql3-BAI3 complex at 2.8 Å resolution. The structure reveals a hexameric configuration, where C1ql3 forms a central homotrimer that effectively captures three BAI3 molecules. These BAI3 molecules fit snugly into the grooves between the trimeric C1q domains of the C1qls, employing calcium ion (Ca)-mediated interactions that differ from previously characterized structures of C1q-like domain-mediated complexes. Furthermore, we conducted mutant analysis and cell surface staining, which confirmed the essential contact residues involved in this interaction. This unique binding mechanism not only enhances our understanding of the C1ql-BAI3-mediated synaptic organization but also sheds light on the functional dynamics of BAI3 in the brain.
History
DepositionFeb 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
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Revision 1.0Feb 5, 2025Data content type: FSC / Data content type: FSC / 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: Adhesion G protein-coupled receptor B3
E: Complement C1q-like protein 3
H: Complement C1q-like protein 3
I: Complement C1q-like protein 3
B: Adhesion G protein-coupled receptor B3
C: Adhesion G protein-coupled receptor B3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,41013
Polymers142,1296
Non-polymers2817
Water1448
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 Adhesion G protein-coupled receptor B3 / Brain-specific angiogenesis inhibitor 3


Mass: 31428.916 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adgrb3, Bai3 / Production host: Homo sapiens (human) / References: UniProt: Q80ZF8
#2: Protein Complement C1q-like protein 3 / C1q and tumor necrosis factor-related protein 13 / C1q/TNF-related protein 13 / CTRP13 / Gliacolin


Mass: 15947.561 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: C1ql3, C1ql, Ctrp13 / Production host: Homo sapiens (human) / References: UniProt: Q9ESN4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
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

ComponentName: Protein complex of mouse C1ql3 with BAI3 adhesion GPCR
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 290 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
4cryoSPARCCTF correction
8PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167880 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0066438
ELECTRON MICROSCOPYf_angle_d0.5348747
ELECTRON MICROSCOPYf_dihedral_angle_d12.5782166
ELECTRON MICROSCOPYf_chiral_restr0.042964
ELECTRON MICROSCOPYf_plane_restr0.0031116

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