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- EMDB-12125: human Teneurin4 Mut C2 -

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Basic information

Entry
Database: EMDB / ID: EMD-12125
Titlehuman Teneurin4 Mut C2
Map dataTeneurin4 mut C2
Sample
  • Organelle or cellular component: human Teneurin4 wt C2 ectodomain
    • Protein or peptide: Teneurin-4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsSynaptic cell adhesion / MEMBRANE PROTEIN
Function / homology
Function and homology information


cardiac cell fate specification / central nervous system myelin formation / positive regulation of myelination / positive regulation of gastrulation / gastrulation with mouth forming second / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cardiac muscle cell proliferation / regulation of myelination / positive regulation of oligodendrocyte differentiation / neuron development ...cardiac cell fate specification / central nervous system myelin formation / positive regulation of myelination / positive regulation of gastrulation / gastrulation with mouth forming second / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cardiac muscle cell proliferation / regulation of myelination / positive regulation of oligodendrocyte differentiation / neuron development / cell adhesion molecule binding / neuron projection / protein heterodimerization activity / signal transduction / protein homodimerization activity / nucleus / plasma membrane / cytoplasm
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 / : / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core ...Teneurin intracellular, N-terminal / Teneurin Intracellular Region / Teneurin N-terminal domain profile. / Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / : / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core / Carboxypeptidase-like, regulatory domain superfamily / EGF-like domain, extracellular / EGF-like domain / 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsMeijer DH / Janssen BJC
Funding support Netherlands, 2 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)722.016.004 Netherlands
European Research Council (ERC)677500 Netherlands
CitationJournal: EMBO J / Year: 2022
Title: Teneurin4 dimer structures reveal a calcium-stabilized compact conformation supporting homomeric trans-interactions.
Authors: Dimphna H Meijer / Cátia P Frias / J Wouter Beugelink / Yanthi N Deurloo / Bert J C Janssen /
Abstract: Establishment of correct synaptic connections is a crucial step during neural circuitry formation. The Teneurin family of neuronal transmembrane proteins promotes cell-cell adhesion via homophilic ...Establishment of correct synaptic connections is a crucial step during neural circuitry formation. The Teneurin family of neuronal transmembrane proteins promotes cell-cell adhesion via homophilic and heterophilic interactions, and is required for synaptic partner matching in the visual and hippocampal systems in vertebrates. It remains unclear how individual Teneurins form macromolecular cis- and trans-synaptic protein complexes. Here, we present a 2.7 Å cryo-EM structure of the dimeric ectodomain of human Teneurin4. The structure reveals a compact conformation of the dimer, stabilized by interactions mediated by the C-rich, YD-shell, and ABD domains. A 1.5 Å crystal structure of the C-rich domain shows three conserved calcium binding sites, and thermal unfolding assays and SAXS-based rigid-body modeling demonstrate that the compactness and stability of Teneurin4 dimers are calcium-dependent. Teneurin4 dimers form a more extended conformation in conditions that lack calcium. Cellular assays reveal that the compact cis-dimer is compatible with homomeric trans-interactions. Together, these findings support a role for teneurins as a scaffold for macromolecular complex assembly and the establishment of cis- and trans-synaptic interactions to construct functional neuronal circuits.
History
DepositionDec 16, 2020-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
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: 0.028
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ban
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12125.png

Downloads & links

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Map

FileDownload / File: emd_12125.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTeneurin4 mut C2
Voxel sizeX=Y=Z: 0.842 Å
Density
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.1314694 - 0.20797794
Average (Standard dev.)0.000033407592 (±0.005186096)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 303.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8420.8420.842
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z303.120303.120303.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1310.2080.000

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Supplemental data

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Mask #1

Fileemd_12125_msk_1.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 : human Teneurin4 wt C2 ectodomain

EntireName: human Teneurin4 wt C2 ectodomain
Components
  • Organelle or cellular component: human Teneurin4 wt C2 ectodomain
    • Protein or peptide: Teneurin-4
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: human Teneurin4 wt C2 ectodomain

SupramoleculeName: human Teneurin4 wt C2 ectodomain / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Teneurin-4

MacromoleculeName: Teneurin-4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 217.699188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METACGDSKD NDGDGLVDCM DPDCCLQPLC HINPLCLGSP NPLDIIQETQ VPVSQQNLHS FYDRIKFLVG RDSTHIIPGE NPFDGGHAC VIRGQVMTSD GTPLVGVNIS FVNNPLFGYT ISRQDGSFDL VTNGGISIIL RFERAPFITQ EHTLWLPWDR F FVMETIIM ...String:
METACGDSKD NDGDGLVDCM DPDCCLQPLC HINPLCLGSP NPLDIIQETQ VPVSQQNLHS FYDRIKFLVG RDSTHIIPGE NPFDGGHAC VIRGQVMTSD GTPLVGVNIS FVNNPLFGYT ISRQDGSFDL VTNGGISIIL RFERAPFITQ EHTLWLPWDR F FVMETIIM RHEENEIPSC DLSNFARPNP VVSPSPLTSF ASSCAEKGPI VPEIQALQEE ISISGCKMRL SYLSSRTPGY KS VLRISLT HPTIPFNLMK VHLMVAVEGR LFRKWFAAAP DLSYYFIWDK TDVYNQKVFG LSEAFVSVGY EYESCPDLIL WEK RTTVLQ GYEIDASKLG GWSLDKHHAL NIQSGILHKG NGENQFVSQQ PPVIGSIMGN GRRRSISCPS CNGLADGNKL LAPV ALTCG SDGSLYVGDF NYIRRIFPSG NVTNILELRN KDFRHSHSPA HKYYLATDPM SGAVFLSDSN SRRVFKIKST VVVKD LVKN SEVVAGTGDQ CLPFDDTRCG DGGKATEATL TNPRGITVDK FGLIYFVDGT MIRRIDQNGI ISTLLGSNDL TSARPL SCD SVMDISQVHL EWPTDLAINP MDNSLYVLDN NVVLQISENH QVRIVAGRPM HCQVPGIDHF LLSKVAIHAT LESATAL AV SHNGVLYIAE TDEKKINRIR QVTTSGEISL VAGAPSGCDC KNDANCDCFS GDDGYAKDAK LNTPSSLAVC ADGELYVA D LGNIRIRFIR KNKPFLNTQN MYELSSPIDQ ELYLFDTTGK HLYTQSLPTG DYLYNFTYTG DGDITLITDN NGNMVNVRR DSTGMPLWLV VPDGQVYWVT MGTNSALKSV TTQGHELAMM TYHGNSGLLA TKSNENGWTT FYEYDSFGRL TNVTFPTGQV SSFRSDTDS SVHVQVETSS KDDVTITTNL SASGAFYTLL QDQVRNSYYI GADGSLRLLL ANGMEVALQT EPHLLAGTVN P TVGKRNVT LPIDNGLNLV EWRQRKEQAR GQVTVFGRRL RVHNRNLLSL DFDRVTRTEK IYDDHRKFTL RILYDQAGRP SL WSPSSRL NGVNVTYSPG GYIAGIQRGI MSERMEYDQA GRITSRIFAD GKTWSYTYLE KSMVLLLHSQ RQYIFEFDKN DRL SSVTMP NVARQTLETI RSVGYYRNIY QPPEGNASVI QDFTEDGHLL HTFYLGTGRR VIYKYGKLSK LAETLYDTTK VSFT YDETA GMLKTINLQN EGFTCTIRYR QIGPLIDRQI FRFTEEGMVN ARFDYNYDNS FRVTSMQAVI NETPLPIDLY RYDDV SGKT EQFGKFGVIY YDINQIITTA VMTHTKHFDA YGRMKEVQYE IFRSLMYWMT VQYDNMGRVV KKELKVGPYA NTTRYS YEY DADGQLQTVS INDKPLWRYS YDLNGNLHLL SPGNSARLTP LRYDIRDRIT RLGDVQYKMD EDGFLRQRGG DIFEYNS AG LLIKAYNRAG SWSVRYRYDG LGRRVSSKSS HSHHLQFFYA DLTNPTKVTH LYNHSSSEIT SLYYDLQGHL FAMELSSG D EFYIACDNIG TPLAVFSGTG LMIKQILYTA YGEIYMDTNP NFQIIIGYHG GLYDPLTKLV HMGRRDYDVL AGRWTSPDH ELWKHLSSSN VMPFNLYMFK NNNPISNSQD IKCFMTDVNS WLLTFGFQLH NVIPGYPKPD MDAMEPSYEL IHTQMKTQEW DNSKSILGV QCEVQKQLKA FVTLERFDQL YGSTITSCQQ APKTKKFASS GSVFGKGVKF ALKDGRVTTD IICVANEDGR R VAAILNHA HYLENLHFTI DGVDTHYFVK PGPSEGDLAI LGLSGGRRTL ENGVNVTVSQ INTVLNGRTR RYTDIQLQYG AL CLNTRYG TTLDEEKARV LELARQRAVR QAWAREQQRL REGEEGLRAW TEGEKQQVLS TGRVQGYDGF FVISVEQYPE LSD SANNIH FMRQSE

UniProtKB: Teneurin-4

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 14 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

Concentration0.075 mg/mL
BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Initial model from data
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242300
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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