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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


postsynaptic density assembly / 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 / neurotransmitter receptor localization to postsynaptic specialization membrane ...postsynaptic density assembly / 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 / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of dendrite morphogenesis / neuron remodeling / regulation of synapse organization / synaptic cleft / GTPase activator activity / hippocampal mossy fiber to CA3 synapse / negative regulation of angiogenesis / 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 / GPCR-Autoproteolysis INducing (GAIN) domain / 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 / GPCR-Autoproteolysis INducing (GAIN) domain / 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 / Collagen triple helix repeat (20 copies) / Thrombospondin type-1 (TSP1) repeat superfamily / 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: To Be Published
Title: Complex structure of C1ql3 with BAI3
Authors: Miao, Y. / Sudhof, T.C.
History
DepositionFeb 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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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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