+Open data
-Basic information
Entry | Database: PDB / ID: 6cmx | |||||||||
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Title | Human Teneurin 2 extra-cellular region | |||||||||
Components | Teneurin-2 | |||||||||
Keywords | MEMBRANE PROTEIN / Teneurin / CNS | |||||||||
Function / homology | Function and homology information retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / neuron development / cell adhesion molecule binding / filopodium / PML body / cell-cell adhesion / cell-cell junction / cell junction ...retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / neuron development / cell adhesion molecule binding / filopodium / PML body / cell-cell adhesion / cell-cell junction / cell junction / growth cone / postsynaptic membrane / dendritic spine / neuron projection / protein heterodimerization activity / signaling receptor binding / dendrite / calcium ion binding / synapse / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / protein homodimerization activity / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Shalev-Benami, M. / Li, J. / Sudhof, T. / Skiniotis, G. / Arac, D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell / Year: 2018 Title: Structural Basis for Teneurin Function in Circuit-Wiring: A Toxin Motif at the Synapse. Authors: Jingxian Li / Moran Shalev-Benami / Richard Sando / Xian Jiang / Amanuel Kibrom / Jie Wang / Katherine Leon / Christopher Katanski / Olha Nazarko / Yue C Lu / Thomas C Südhof / Georgios ...Authors: Jingxian Li / Moran Shalev-Benami / Richard Sando / Xian Jiang / Amanuel Kibrom / Jie Wang / Katherine Leon / Christopher Katanski / Olha Nazarko / Yue C Lu / Thomas C Südhof / Georgios Skiniotis / Demet Araç / Abstract: Teneurins (TENs) are cell-surface adhesion proteins with critical roles in tissue development and axon guidance. Here, we report the 3.1-Å cryoelectron microscopy structure of the human TEN2 ...Teneurins (TENs) are cell-surface adhesion proteins with critical roles in tissue development and axon guidance. Here, we report the 3.1-Å cryoelectron microscopy structure of the human TEN2 extracellular region (ECR), revealing a striking similarity to bacterial Tc-toxins. The ECR includes a large β barrel that partially encapsulates a C-terminal domain, which emerges to the solvent through an opening in the mid-barrel region. An immunoglobulin (Ig)-like domain seals the bottom of the barrel while a β propeller is attached in a perpendicular orientation. We further show that an alternatively spliced region within the β propeller acts as a switch to regulate trans-cellular adhesion of TEN2 to latrophilin (LPHN), a transmembrane receptor known to mediate critical functions in the central nervous system. One splice variant activates trans-cellular signaling in a LPHN-dependent manner, whereas the other induces inhibitory postsynaptic differentiation. These results highlight the unusual structural organization of TENs giving rise to their multifarious functions. | |||||||||
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 | 6cmx.cif.gz | 261.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cmx.ent.gz | 190.5 KB | Display | PDB format |
PDBx/mmJSON format | 6cmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cmx_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6cmx_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6cmx_validation.xml.gz | 44.8 KB | Display | |
Data in CIF | 6cmx_validation.cif.gz | 67 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/6cmx ftp://data.pdbj.org/pub/pdb/validation_reports/cm/6cmx | HTTPS FTP |
-Related structure data
Related structure data | 7526MC 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
#1: Protein | Mass: 224005.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TENM2, KIAA1127, ODZ2, TNM2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High-Five / References: UniProt: Q9NT68*PLUS | ||||
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#2: 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 | ||||
#3: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose / 6alpha-alpha-mannobiose | ||||
#4: Sugar | ChemComp-NAG / #5: Sugar | Has protein modification | Y | |
-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: Teneurin 2 extra-cellular region / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.215 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298.15 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: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 426107 / Symmetry type: POINT | ||||||||||||||||||||||||
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