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- EMDB-19409: Mouse teneurin-3 compact dimer - A1B0 isoform -

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Basic information

Entry
Database: EMDB / ID: EMD-19409
TitleMouse teneurin-3 compact dimer - A1B0 isoform
Map dataFull map of the mouse teneurin-3 A1B0 isoform compact dimer conformation
Sample
  • Complex: mouse teneurin-3 A1B0 isoform ectodomain compact dimer
KeywordsSynaptic cell adhesion molecule / Homodimer / Cis-synaptic / CELL ADHESION
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGogou C / Meijer DH
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)722.016.004 Netherlands
CitationJournal: Nat Commun / Year: 2024
Title: Alternative splicing controls teneurin-3 compact dimer formation for neuronal recognition.
Authors: Christos Gogou / J Wouter Beugelink / Cátia P Frias / Leanid Kresik / Natalia Jaroszynska / Uwe Drescher / Bert J C Janssen / Robert Hindges / Dimphna H Meijer /
Abstract: Neuronal network formation is facilitated by recognition between synaptic cell adhesion molecules at the cell surface. Alternative splicing of cell adhesion molecules provides additional specificity ...Neuronal network formation is facilitated by recognition between synaptic cell adhesion molecules at the cell surface. Alternative splicing of cell adhesion molecules provides additional specificity in forming neuronal connections. For the teneurin family of cell adhesion molecules, alternative splicing of the EGF-repeats and NHL domain controls synaptic protein-protein interactions. Here we present cryo-EM structures of the compact dimeric ectodomain of two teneurin-3 isoforms that harbour the splice insert in the EGF-repeats. This dimer is stabilised by an EGF8-ABD contact between subunits. Cryo-EM reconstructions of all four splice variants, together with SAXS and negative stain EM, reveal compacted dimers for each, with variant-specific dimeric arrangements. This results in specific trans-cellular interactions, as tested in cell clustering and stripe assays. The compact conformations provide a structural basis for teneurin homo- and heterophilic interactions. Altogether, our findings demonstrate how alternative splicing results in rearrangements of the dimeric subunits, influencing neuronal recognition and likely circuit wiring.
History
DepositionJan 14, 2024-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19409.png

Downloads & links

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Map

FileDownload / File: emd_19409.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map of the mouse teneurin-3 A1B0 isoform compact dimer conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 267.52 Å		0.84 Å/pix.
x 320 pix.
= 267.52 Å		0.84 Å/pix.
x 320 pix.
= 267.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0104
Minimum - Maximum-0.015440402 - 0.03576998
Average (Standard dev.)0.00013822444 (±0.0019269488)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 267.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of the mouse teneurin-3 A1B0 isoform...

Fileemd_19409_half_map_1.map
AnnotationHalf map of the mouse teneurin-3 A1B0 isoform compact dimer conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of the mouse teneurin-3 A1B0 isoform...

Fileemd_19409_half_map_2.map
AnnotationHalf map of the mouse teneurin-3 A1B0 isoform compact dimer conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mouse teneurin-3 A1B0 isoform ectodomain compact dimer

EntireName: mouse teneurin-3 A1B0 isoform ectodomain compact dimer
Components
  • Complex: mouse teneurin-3 A1B0 isoform ectodomain compact dimer

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Supramolecule #1: mouse teneurin-3 A1B0 isoform ectodomain compact dimer

SupramoleculeName: mouse teneurin-3 A1B0 isoform ectodomain compact dimer
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 536.96 KDa

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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

Concentration0.5 mg/mL
BufferpH: 7.8 / Details: 20 mM HEPES, 150 mM NaCl, 2mM CaCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

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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: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23002
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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