+Open data
-Basic information
Entry | Database: PDB / ID: 6vhh | ||||||||||||
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Title | Human Teneurin-2 and human Latrophilin-3 binary complex | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Adhesion GPCR / synapse / Teneurin / Lphn | ||||||||||||
Function / homology | Function and homology information retrograde trans-synaptic signaling by trans-synaptic protein complex / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / : / neuron development / synapse assembly / cell adhesion molecule binding / filopodium / G protein-coupled receptor activity ...retrograde trans-synaptic signaling by trans-synaptic protein complex / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / : / neuron development / synapse assembly / cell adhesion molecule binding / filopodium / G protein-coupled receptor activity / axon guidance / neuron migration / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell-cell adhesion / PML body / cell-cell junction / cell junction / growth cone / postsynaptic membrane / carbohydrate binding / dendritic spine / cell surface receptor signaling pathway / neuron projection / G protein-coupled receptor signaling pathway / protein heterodimerization activity / axon / signaling receptor binding / dendrite / glutamatergic synapse / synapse / calcium ion binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / protein homodimerization activity / membrane / nucleus / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å | ||||||||||||
Authors | Xie, Y. / Li, J. / Arac, D. / Zhao, M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2020 Title: Alternative splicing controls teneurin-latrophilin interaction and synapse specificity by a shape-shifting mechanism. Authors: Jingxian Li / Yuan Xie / Shaleeka Cornelius / Xian Jiang / Richard Sando / Szymon P Kordon / Man Pan / Katherine Leon / Thomas C Südhof / Minglei Zhao / Demet Araç / Abstract: The trans-synaptic interaction of the cell-adhesion molecules teneurins (TENs) with latrophilins (LPHNs/ADGRLs) promotes excitatory synapse formation when LPHNs simultaneously interact with FLRTs. ...The trans-synaptic interaction of the cell-adhesion molecules teneurins (TENs) with latrophilins (LPHNs/ADGRLs) promotes excitatory synapse formation when LPHNs simultaneously interact with FLRTs. Insertion of a short alternatively-spliced region within TENs abolishes the TEN-LPHN interaction and switches TEN function to specify inhibitory synapses. How alternative-splicing regulates TEN-LPHN interaction remains unclear. Here, we report the 2.9 Å resolution cryo-EM structure of the TEN2-LPHN3 complex, and describe the trimeric TEN2-LPHN3-FLRT3 complex. The structure reveals that the N-terminal lectin domain of LPHN3 binds to the TEN2 barrel at a site far away from the alternatively spliced region. Alternative-splicing regulates the TEN2-LPHN3 interaction by hindering access to the LPHN-binding surface rather than altering it. Strikingly, mutagenesis of the LPHN-binding surface of TEN2 abolishes the LPHN3 interaction and impairs excitatory but not inhibitory synapse formation. These results suggest that a multi-level coincident binding mechanism mediated by a cryptic adhesion complex between TENs and LPHNs regulates synapse specificity. | ||||||||||||
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 | 6vhh.cif.gz | 356 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vhh.ent.gz | 264 KB | Display | PDB format |
PDBx/mmJSON format | 6vhh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/6vhh ftp://data.pdbj.org/pub/pdb/validation_reports/vh/6vhh | HTTPS FTP |
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-Related structure data
Related structure data | 21205MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 216254.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TENM2, KIAA1127, ODZ2, TNM2 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NT68 |
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#2: Protein | Mass: 95209.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADGRL3, KIAA0768, LEC3, LPHN3 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9HAR2 |
-Sugars , 4 types, 8 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | |
-Details
Has ligand of interest | N |
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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: Binary complex of human Teneurin-2 with human Latrophilin-3 extracellular domain Type: COMPLEX Details: The binary complex includes human Teneurin2 (TENM2) (Teneurin without alternative splice sequence NKEFKHS) and human Latrophilin3 (LPHN3/ADGRL3) with an alternative splice sequence KVEQK ...Details: The binary complex includes human Teneurin2 (TENM2) (Teneurin without alternative splice sequence NKEFKHS) and human Latrophilin3 (LPHN3/ADGRL3) with an alternative splice sequence KVEQK between lectin domain and olfactomedin domain. Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.314 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) / Cell: Hi5 |
Buffer solution | pH: 8.5 |
Specimen | Conc.: 2.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4.2 sec. / Electron dose: 60.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 5402 |
-Processing
EM software |
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CTF correction | Details: CTF correction was done in Relion reconstruction / Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4475958 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 436208 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.62 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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