+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12127 | |||||||||
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Title | human Teneurin4 Mut C-rich | |||||||||
Map data | human Teneurin4 mut C-rich | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Meijer DH / Janssen BJC | |||||||||
Funding support | Netherlands, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12127.map.gz | 110.1 MB | EMDB map data format | |
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Header (meta data) | emd-12127-v30.xml emd-12127.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12127_fsc.xml | 16.6 KB | Display | FSC data file |
Images | emd_12127.png | 40.4 KB | ||
Masks | emd_12127_msk_1.map | 178 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12127 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12127 | HTTPS FTP |
-Validation report
Summary document | emd_12127_validation.pdf.gz | 369.9 KB | Display | EMDB validaton report |
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Full document | emd_12127_full_validation.pdf.gz | 369.5 KB | Display | |
Data in XML | emd_12127_validation.xml.gz | 13 KB | Display | |
Data in CIF | emd_12127_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12127 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12127 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12127.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | human Teneurin4 mut C-rich | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.842 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12127_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human Teneurin4 mut C1 ectodomain
Entire | Name: human Teneurin4 mut C1 ectodomain |
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Components |
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-Supramolecule #1: human Teneurin4 mut C1 ectodomain
Supramolecule | Name: human Teneurin4 mut C1 ectodomain / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293E |
-Supramolecule #2: human Teneurin4 mut C1 c-rich focussed
Supramolecule | Name: human Teneurin4 mut C1 c-rich focussed / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293E |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.075 mg/mL |
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Buffer | pH: 7.8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |