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- EMDB-43605: Complex structure of mouse C1ql3 with BAI3 -

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Basic information

Entry
Database: EMDB / ID: EMD-43605
TitleComplex structure of mouse C1ql3 with BAI3
Map data
Sample
  • Complex: Protein complex of mouse C1ql3 with BAI3 adhesion GPCR
    • Protein or peptide: Adhesion G protein-coupled receptor B3
    • Protein or peptide: Complement C1q-like protein 3
  • Ligand: CALCIUM ION
  • Ligand: water
Keywordsadhesion GPCR / C1q like proteins / CELL ADHESION
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsMiao Y / Sudhof TC
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Complex structure of C1ql3 with BAI3
Authors: Miao Y / Sudhof TC
History
DepositionFeb 2, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43605.png

Downloads & links

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Map

FileDownload / File: emd_43605.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 300 pix.
= 195.9 Å		0.65 Å/pix.
x 300 pix.
= 195.9 Å		0.65 Å/pix.
x 300 pix.
= 195.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.653 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.109
Minimum - Maximum-0.6568854 - 1.029779
Average (Standard dev.)-0.0003078969 (±0.023780776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 195.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43605_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43605_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Protein complex of mouse C1ql3 with BAI3 adhesion GPCR

EntireName: Protein complex of mouse C1ql3 with BAI3 adhesion GPCR
Components
  • Complex: Protein complex of mouse C1ql3 with BAI3 adhesion GPCR
    • Protein or peptide: Adhesion G protein-coupled receptor B3
    • Protein or peptide: Complement C1q-like protein 3
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: Protein complex of mouse C1ql3 with BAI3 adhesion GPCR

SupramoleculeName: Protein complex of mouse C1ql3 with BAI3 adhesion GPCR
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Adhesion G protein-coupled receptor B3

MacromoleculeName: Adhesion G protein-coupled receptor B3 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 31.428916 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DFWCSTLVKG VIYGSYSVSE MFPKNFTNCT WTLENPDPTK YSIYLKFSKK DLSCSNFSLL AYQFDHFSHE KIKDLLRKNH SIMQLCSSK NAFVFLQYDK NFIQIRRVFP TDFPGLQKKV EEDQKSFFEF LVLNKVSPSQ FGCHVLCTWL ESCLKSENGR T ESCGIMYT ...String:
DFWCSTLVKG VIYGSYSVSE MFPKNFTNCT WTLENPDPTK YSIYLKFSKK DLSCSNFSLL AYQFDHFSHE KIKDLLRKNH SIMQLCSSK NAFVFLQYDK NFIQIRRVFP TDFPGLQKKV EEDQKSFFEF LVLNKVSPSQ FGCHVLCTWL ESCLKSENGR T ESCGIMYT KCTCPQHLGE WGIDDQSLVL LNNVVLPLNE QTEGCLTQEL QTTQVCNLTR EAKRPPKEEF GMMGDHTIKS QR PRSVHEK RVPQEQADAA KFMAQTGAAA LEVLFQ

UniProtKB: Adhesion G protein-coupled receptor B3

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Macromolecule #2: Complement C1q-like protein 3

MacromoleculeName: Complement C1q-like protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 15.947561 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DASHHHHHHS TVPKIAFYAG LKRQHEGYEV LKFDDVVTNL GNHYDPTTGK FTCSIPGIYF FTYHVLMRGG DGTSMWADLC KNNQVRASA IAQDADQNYD YASNSVVLHL EPGDEVYIKL DGGKAHGGNN NKYSTFSGFI IYAD

UniProtKB: Complement C1q-like protein 3

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 7 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 290 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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Alpha Fold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 167880
Initial angle assignmentType: OTHER / Details: stochastic gradient descent
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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