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- EMDB-18891: Mouse teneurin-3 non-compact subunit - A0B0 isoform -

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Basic information

Entry
Database: EMDB / ID: EMD-18891
TitleMouse teneurin-3 non-compact subunit - A0B0 isoform
Map dataMap of the mouse teneurin-3 A0B0 isoform ectodomain non-compact subunit
Sample
  • Complex: Mouse teneurin-3 A0B0 isoform ectodomain subunit
    • Protein or peptide: Teneurin-3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSynaptic cell adhesion molecule / Homodimer / Cis-synaptic / CELL ADHESION
Function / homology
Function and homology information


regulation of homophilic cell adhesion / camera-type eye morphogenesis / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / neuron development / cell adhesion molecule binding / positive regulation of neuron projection development / neuron projection / protein heterodimerization activity / axon ...regulation of homophilic cell adhesion / camera-type eye morphogenesis / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / neuron development / cell adhesion molecule binding / positive regulation of neuron projection development / neuron projection / protein heterodimerization activity / axon / signal transduction / protein homodimerization activity / membrane / identical protein binding / plasma membrane
Similarity search - Function
Teneurin intracellular, N-terminal / Teneurin Intracellular Region / Teneurin N-terminal domain profile. / Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / YD repeat / Rhs repeat-associated core / Carboxypeptidase-like, regulatory domain superfamily / Six-bladed beta-propeller, TolB-like / Epidermal growth factor-like domain. ...Teneurin intracellular, N-terminal / Teneurin Intracellular Region / Teneurin N-terminal domain profile. / Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / YD repeat / Rhs repeat-associated core / Carboxypeptidase-like, regulatory domain superfamily / Six-bladed beta-propeller, TolB-like / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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
DepositionNov 15, 2023-
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_18891.png

Downloads & links

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Map

FileDownload / File: emd_18891.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the mouse teneurin-3 A0B0 isoform ectodomain non-compact subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 240 pix.
= 206.16 Å		0.86 Å/pix.
x 240 pix.
= 206.16 Å		0.86 Å/pix.
x 240 pix.
= 206.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.859 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0098
Minimum - Maximum-0.031620104 - 0.06657247
Average (Standard dev.)0.00020827292 (±0.0027733473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 206.16 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 A0B0 isoform...

Fileemd_18891_half_map_1.map
AnnotationHalf map of the mouse teneurin-3 A0B0 isoform ectodomain non-compact subunit
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 A0B0 isoform...

Fileemd_18891_half_map_2.map
AnnotationHalf map of the mouse teneurin-3 A0B0 isoform ectodomain non-compact subunit
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 A0B0 isoform ectodomain subunit

EntireName: Mouse teneurin-3 A0B0 isoform ectodomain subunit
Components
  • Complex: Mouse teneurin-3 A0B0 isoform ectodomain subunit
    • Protein or peptide: Teneurin-3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Mouse teneurin-3 A0B0 isoform ectodomain subunit

SupramoleculeName: Mouse teneurin-3 A0B0 isoform ectodomain subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 532.92 KDa

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Macromolecule #1: Teneurin-3

MacromoleculeName: Teneurin-3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 266.692844 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MARPLCTLLL LMATLAGALA GSHHHHHHGS QTENDTFENG KVNSDTVPTN TVSLPSGDNG KLGGFTHENN TIDSGELDIG RRAIQEVPP GIFWRSQLFI DQPQFLKFNI SLQKDALIGV YGRKGLPPSH TQYDFVELLD GSRLIAREQR NLVESERAGR Q ARSVSLHE ...String:
MARPLCTLLL LMATLAGALA GSHHHHHHGS QTENDTFENG KVNSDTVPTN TVSLPSGDNG KLGGFTHENN TIDSGELDIG RRAIQEVPP GIFWRSQLFI DQPQFLKFNI SLQKDALIGV YGRKGLPPSH TQYDFVELLD GSRLIAREQR NLVESERAGR Q ARSVSLHE AGFIQYLDSG IWHLAFYNDG KNPEQVSFNT IVIESVVECP RNCHGNGECV SGTCHCFPGF LGPDCSRAAC PV LCSGNGQ YSKGRCLCFS GWKGTECDVP TTQCIDPQCG GRGICIMGSC ACNSGYKGEN CEEADCLDPG CSNHGVCIHG ECH CNPGWG GSNCEILKTM CADQCSGHGT YLQESGSCTC DPNWTGPDCS NEICSVDCGS HGVCMGGSCR CEEGWTGPAC NQRA CHPRC AEHGTCKDGK CECSQGWNGE HCTIEGCPGL CNSNGRCTLD QNGWHCVCQP GWRGAGCDVA METLCTDSKD NEGDG LIDC MDPDCCLQSS CQNQPYCRGL PDPQDIISQS LQTPSQQAAK SFYDRISFLI GSDSTHVLPG ESPFNKSLAS VIRGQV LTA DGTPLIGVNV SFLHYSEYGY TITRQDGMFD LVANGGASLT LVFERSPFLT QYHTVWIPWN VFYVMDTLVM KKEENDI PS CDLSGFVRPS PIIVSSPLST FFRSSPEDSP IIPETQVLHE ETTIPGTDLK LSYLSSRAAG YKSVLKITMT QAVIPFNL M KVHLMVAVVG RLFQKWFPAS PNLAYTFIWD KTDAYNQKVY GLSEAVVSVG YEYESCLDLT LWEKRTAVLQ GYELDASNM GGWTLDKHHV LDVQNGILYK GNGENQFISQ QPPVVSSIMG NGRRRSISCP SCNGQADGNK LLAPVALACG IDGSLYVGDF NYVRRIFPS GNVTSVLELS SNPAHRYYLA TDPVTGDLYV SDTNTRRIYR PKSLTGAKDL TKNAEVVAGT GEQCLPFDEA R CGDGGKAV EATLMSPKGM AIDKNGLIYF VDGTMIRKVD QNGIISTLLG SNDLTSARPL TCDTSMHISQ VRLEWPTDLA IN PMDNSIY VLDNNVVLQI TENRQVRIAA GRPMHCQVPG VEYPVGKHAV QTTLESATAI AVSYSGVLYI TETDEKKINR IRQ VTTDGE ISLVAGIPSE CDCKNDANCD CYQSGDGYAK DAKLNAPSSL AASPDGTLYI ADLGNIRIRA VSKNKPLLNS MNFY EVASP TDQELYIFDI NGTHQYTVSL VTGDYLYNFS YSNDNDVTAV TDSNGNTLRI RRDPNRMPVR VVSPDNQVIW LTIGT NGCL KSMTAQGLEL VLFTYHGNSG LLATKSDETG WTTFFDYDSE GRLTNVTFPT GVVTNLHGDM DKAITVDIES SSREED VSI TSNLSSIDSF YTMVQDQLRN SYQIGYDGSL RIFYASGLDS HYQTEPHVLA GTANPTVAKR NMTLPGENGQ NLVEWRF RK EQAQGKVNVF GRKLRVNGRN LLSVDFDRTT KTEKIYDDHR KFLLRIAYDT SGHPTLWLPS SKLMAVNVTY SSTGQIAS I QRGTTSEKVD YDSQGRIVSR VFADGKTWSY TYLEKSMVLL LHSQRQYIFE YDMWDRLSAI TMPSVARHTM QTIRSIGYY RNIYNPPESN ASIITDYNEE GLLLQTAFLG TSRRVLFKYR RQTRLSEILY DSTRVSFTYD ETAGVLKTVN LQSDGFICTI RYRQIGPLI DRQIFRFSED GMVNARFDYS YDNSFRVTSM QGVINETPLP IDLYQFDDIS GKVEQFGKFG VIYYDINQII S TAVMTYTK HFDAHGRIKE IQYEIFRSLM YWITIQYDNM GRVTKREIKI GPFANTTKYA YEYDVDGQLQ TVYLNEKIMW RY NYDLNGN LHLLNPSSSA RLTPLRYDLR DRITRLGDVQ YRLDEDGFLR QRGTEIFEYS SKGLLTRVYS KGSGWTVIYR YDG LGRRVS SKTSLGQHLQ FFYADLTYPT RITHVYNHSS SEITSLYYDL QGHLFAMEIS SGDEFYIASD NTGTPLAVFS SNGL MLKQI QYTAYGEIYF DSNVDFQLVI GFHGGLYDPL TKLIHFGERD YDILAGRWTT PDIEIWKRIG KDPAPFNLYM FRNNN PASK IHDVKDYITD VNSWLVTFGF HLHNAIPGFP VPKFDLTEPS YELVKSQQWE DVPPIFGVQQ QVARQAKAFL SLGKMA EVQ VSRRKAGAEQ SWLWFATVKS LIGKGVMLAV SQGRVQTNVL NIANEDCIKV AAVLNNAFYL ENLHFTIEGK DTHYFIK TT TPESDLGTLR LTSGRKALEN GINVTVSQST TVVNGRTRRF ADVEMQFGAL ALHVRYGMTL DEEKARILEQ ARQRALAR A WAREQQRVRD GEEGARLWTE GEKRQLLSAG KVQGYDGYYV LSVEQYPELA DSANNIQFLR QSEIGKRAAA

UniProtKB: Teneurin-3

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66637
FSC plot (resolution estimation)

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