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- EMDB-4219: Teneurin3 monomer -

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Basic information

Entry
Database: EMDB / ID: EMD-4219
TitleTeneurin3 monomer
Map dataTeneurin3 monomer map
Sample
  • Organelle or cellular component: Teneurin3 monomer
    • Protein or peptide: Odz3 protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNeuronal cell adhesion / bacterial toxin-like / CELL ADHESION
Function / homology
Function and homology information


regulation of homophilic cell adhesion / synaptic membrane adhesion / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / neuron development / presynaptic active zone membrane / cell adhesion molecule binding / cell projection / positive regulation of neuron projection development / neuron projection ...regulation of homophilic cell adhesion / synaptic membrane adhesion / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / neuron development / presynaptic active zone membrane / cell adhesion molecule binding / cell projection / positive regulation of neuron projection development / neuron projection / protein heterodimerization activity / axon / glutamatergic synapse / signal transduction / protein homodimerization activity / identical protein binding / membrane / 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 ...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
Odz3 protein / Teneurin-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsJanssen BJC / Meijer DHM
Funding support Netherlands, 2 items
OrganizationGrant numberCountry
European Molecular Biology Organization125-2015 Netherlands
Netherlands Organisation for Scientific Research723.012.002 Netherlands
CitationJournal: Nat Commun / Year: 2018
Title: Structures of Teneurin adhesion receptors reveal an ancient fold for cell-cell interaction.
Authors: Verity A Jackson / Dimphna H Meijer / Maria Carrasquero / Laura S van Bezouwen / Edward D Lowe / Colin Kleanthous / Bert J C Janssen / Elena Seiradake /
Abstract: Teneurins are ancient cell-cell adhesion receptors that are vital for brain development and synapse organisation. They originated in early metazoan evolution through a horizontal gene transfer event ...Teneurins are ancient cell-cell adhesion receptors that are vital for brain development and synapse organisation. They originated in early metazoan evolution through a horizontal gene transfer event when a bacterial YD-repeat toxin fused to a eukaryotic receptor. We present X-ray crystallography and cryo-EM structures of two Teneurins, revealing a ~200 kDa extracellular super-fold in which eight sub-domains form an intricate structure centred on a spiralling YD-repeat shell. An alternatively spliced loop, which is implicated in homophilic Teneurin interaction and specificity, is exposed and thus poised for interaction. The N-terminal side of the shell is 'plugged' via a fibronectin-plug domain combination, which defines a new class of YD proteins. Unexpectedly, we find that these proteins are widespread amongst modern bacteria, suggesting early metazoan receptor evolution from a distinct class of proteins, which today includes both bacterial proteins and eukaryotic Teneurins.
History
DepositionDec 18, 2017-
Header (metadata) releaseMar 28, 2018-
Map releaseMar 28, 2018-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6fay
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4219.png

Downloads & links

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Map

FileDownload / File: emd_4219.map.gz / Format: CCP4 / Size: 206 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTeneurin3 monomer map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 378 pix.
= 389.34 Å		1.03 Å/pix.
x 378 pix.
= 389.34 Å		1.03 Å/pix.
x 378 pix.
= 389.34 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-0.8135529 - 2.1907325
Average (Standard dev.)0.0021192243 (±0.037093192)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions378378378
Spacing378378378
CellA=B=C: 389.34 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z378378378
origin x/y/z0.0000.0000.000
length x/y/z389.340389.340389.340
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS378378378
D min/max/mean-0.8142.1910.002

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Supplemental data

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Half map: Half-map 1 for Teneurin3 monomer

Fileemd_4219_half_map_1.map
AnnotationHalf-map 1 for Teneurin3 monomer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 for Teneurin3 monomer

Fileemd_4219_half_map_2.map
AnnotationHalf-map 2 for Teneurin3 monomer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Teneurin3 monomer

EntireName: Teneurin3 monomer
Components
  • Organelle or cellular component: Teneurin3 monomer
    • Protein or peptide: Odz3 protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Teneurin3 monomer

SupramoleculeName: Teneurin3 monomer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Odz3 protein

MacromoleculeName: Odz3 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 211.429734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSFYDRISFL IGSDSTHVLP GESPFNKSLA SVIRGQVLTA DGTPLIGVNV SFLHYSEYGY TITRQDGMFD LVANGGASLT LVFERSPFL TQYHTVWIPW NVFYVMDTLV MKKEENDIPS CDLSGFVRPS PIIVSSPLST FFRSSPEDSP IIPETQVLHE E TTIPGTDL ...String:
GSFYDRISFL IGSDSTHVLP GESPFNKSLA SVIRGQVLTA DGTPLIGVNV SFLHYSEYGY TITRQDGMFD LVANGGASLT LVFERSPFL TQYHTVWIPW NVFYVMDTLV MKKEENDIPS CDLSGFVRPS PIIVSSPLST FFRSSPEDSP IIPETQVLHE E TTIPGTDL KLSYLSSRAA GYKSVLKITM TQAVIPFNLM KVHLMVAVVG RLFQKWFPAS PNLAYTFIWD KTDAYNQKVY GL SEAVVSV GYEYESCLDL TLWEKRTAVL QGYELDASNM GGWTLDKHHV LDVQNGILYK GNGENQFISQ QPPVVSSIMG NGR RRSISC PSCNGQADGN KLLAPVALAC GIDGSLYVGD FNYVRRIFPS GNVTSVLELS SNPAHRYYLA TDPVTGDLYV SDTN TRRIY RPKSLTGAKD LTKNAEVVAG TGEQCLPFDE ARCGDGGKAV EATLMSPKGM AIDKNGLIYF VDGTMIRKVD QNGII STLL GSNDLTSARP LTCDTSMHIS QVRLEWPTDL AINPMDNSIY VLDNNVVLQI TENRQVRIAA GRPMHCQVPG VEYPVG KHA VQTTLESATA IAVSYSGVLY ITETDEKKIN RIRQVTTDGE ISLVAGIPSE CDCKNDANCD CYQSGDGYAK DAKLNAP SS LAASPDGTLY IADLGNIRIR AVSKNKPLLN SMNFYEVASP TDQELYIFDI NGTHQYTVSL VTGDYLYNFS YSNDNDVT A VTDSNGNTLR IRRDPNRMPV RVVSPDNQVI WLTIGTNGCL KSMTAQGLEL VLFTYHGNSG LLATKSDETG WTTFFDYDS EGRLTNVTFP TGVVTNLHGD MDKAITVDIE SSSREEDVSI TSNLSSIDSF YTMVQDQLRN SYQIGYDGSL RIFYASGLDS HYQTEPHVL AGTANPTVAK RNMTLPGENG QNLVEWRFRK EQAQGKVNVF GRKLRVNGRN LLSVDFDRTT KTEKIYDDHR K FLLRIAYD TSGHPTLWLP SSKLMAVNVT YSSTGQIASI QRGTTSEKVD YDSQGRIVSR VFADGKTWSY TYLEKSMVLL LH SQRQYIF EYDMWDRLSA ITMPSVARHT MQTIRSIGYY RNIYNPPESN ASIITDYNEE GLLLQTAFLG TSRRVLFKYR RQT RLSEIL YDSTRVSFTY DETAGVLKTV NLQSDGFICT IRYRQIGPLI DRQIFRFSED GMVNARFDYS YDNSFRVTSM QGVI NETPL PIDLYQFDDI SGKVEQFGKF GVIYYDINQI ISTAVMTYTK HFDAHGRIKE IQYEIFRSLM YWITIQYDNM GRVTK REIK IGPFANTTKY AYEYDVDGQL QTVYLNEKIM WRYNYDLNGN LHLLNPSSSA RLTPLRYDLR DRITRLGDVQ YRLDED GFL RQRGTEIFEY SSKGLLTRVY SKGSGWTVIY RYDGLGRRVS SKTSLGQHLQ FFYADLTYPT RITHVYNHSS SEITSLY YD LQGHLFAMEI SSGDEFYIAS DNTGTPLAVF SSNGLMLKQI QYTAYGEIYF DSNVDFQLVI GFHGGLYDPL TKLIHFGE R DYDILAGRWT TPDIEIWKRI GKDPAPFNLY MFRNNNPASK IHDVKDYITD VNSWLVTFGF HLHNAIPGFP VPKFDLTEP SYELVKSQQW EDVPPIFGVQ QQVARQAKAF LSLGKMAEVQ VSRRKAGAEQ SWLWFATVKS LIGKGVMLAV SQGRVQTNVL NIANEDCIK VAAVLNNAFY LENLHFTIEG KDTHYFIKTT TPESDLGTLR LTSGRKALEN GINVTVSQST TVVNGRTRRF A DVEMQFGA LALHVRYGMT LDEEKARILE QARQRALARA WAREQQRVRD GEEGARLWTE GEKRQLLSAG KVQGYDGYYV LS VEQYPEL ADSANNIQFL RQSEIGKRAS AAAHHHHHH

UniProtKB: Odz3 protein

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.1 mg/mL
BufferpH: 9
Component:
ConcentrationNameFormula
20.0 mMCHES
150.0 mMSodium ChlorideNaCl
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 435755
Startup modelType of model: OTHER / Details: An initial model was generated using cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 287402
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 2 / Avg.num./class: 100000 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6fb3


Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: We have used PDB 6FB3 (same publication) as a template model using Modeller v9.16 followed by manual rebuilding in Coot and real-space refinement using Phenix.
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 126
Output model

PDB-6fay:
Teneurin3 monomer

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