+Open data
-Basic information
Entry | Database: PDB / ID: 7ban | |||||||||
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Title | human Teneurin4 Mut C2 | |||||||||
Components | Teneurin-4 | |||||||||
Keywords | MEMBRANE PROTEIN / Synaptic cell adhesion | |||||||||
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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Meijer, D.H. / Janssen, B.J.C. | |||||||||
Funding support | Netherlands, 2items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ban.cif.gz | 679.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ban.ent.gz | 561.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ban.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ban_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7ban_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7ban_validation.xml.gz | 105.4 KB | Display | |
Data in CIF | 7ban_validation.cif.gz | 160.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/7ban ftp://data.pdbj.org/pub/pdb/validation_reports/ba/7ban | HTTPS FTP |
-Related structure data
Related structure data | 12125MC 7bamC 7baoC 7plpC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 217699.188 Da / Num. of mol.: 2 / Mutation: S2585C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TENM4, KIAA1302, ODZ4, TNM4 / Cell (production host): HEK293E / Production host: Homo sapiens (human) / References: UniProt: Q6N022 #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Chemical | ChemComp-CA / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: human Teneurin4 wt C2 ectodomain / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293E |
Buffer solution | pH: 7.8 |
Specimen | Conc.: 0.075 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 242300 / Symmetry type: POINT | ||||||||||||||||||||||||
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