+Open data
-Basic information
Entry | Database: PDB / ID: 6ska | |||||||||
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Title | Teneurin 2 in complex with Latrophilin 1 Lec-Olf domains | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / adhesion / Odz / Lphn / synapse / neurons / repulsion / olfactomedin / lectin / YD-repeat / complex | |||||||||
Function / homology | Function and homology information latrotoxin receptor activity / positive regulation of synapse maturation / positive regulation of synapse assembly / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / : / toxic substance binding / neuron development / cell adhesion molecule binding / filopodium ...latrotoxin receptor activity / positive regulation of synapse maturation / positive regulation of synapse assembly / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / : / toxic substance binding / neuron development / cell adhesion molecule binding / filopodium / G protein-coupled receptor activity / axon guidance / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell-cell adhesion / PML body / cell-cell junction / presynaptic membrane / cell junction / growth cone / postsynaptic membrane / carbohydrate binding / dendritic spine / cell surface receptor signaling pathway / neuron projection / 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 / protein homodimerization activity / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | Gallus gallus (chicken) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.86 Å | |||||||||
Authors | Chu, A. / Carrasquero, M.A. / Lowe, E. / Seiradake, E. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Cell / Year: 2020 Title: Structural Basis of Teneurin-Latrophilin Interaction in Repulsive Guidance of Migrating Neurons. Authors: Del Toro, D. / Carrasquero-Ordaz, M.A. / Chu, A. / Ruff, T. / Shahin, M. / Jackson, V.A. / Chavent, M. / Berbeira-Santana, M. / Seyit-Bremer, G. / Brignani, S. / Kaufmann, R. / Lowe, E. / ...Authors: Del Toro, D. / Carrasquero-Ordaz, M.A. / Chu, A. / Ruff, T. / Shahin, M. / Jackson, V.A. / Chavent, M. / Berbeira-Santana, M. / Seyit-Bremer, G. / Brignani, S. / Kaufmann, R. / Lowe, E. / Klein, R. / Seiradake, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ska.cif.gz | 862.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ska.ent.gz | 709.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ska.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/6ska ftp://data.pdbj.org/pub/pdb/validation_reports/sk/6ska | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AD
#1: Protein | Mass: 206155.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: TENM2, ODZ2, TNM2 / Production host: Homo sapiens (human) / References: UniProt: Q9DER5 |
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#2: Protein | Mass: 39919.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adgrl1, Kiaa0821, Lec2, Lphn1 / Production host: Homo sapiens (human) / References: UniProt: Q80TR1 |
-Sugars , 3 types, 11 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]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 | ||
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#4: 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 #5: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 1 molecules
#6: Chemical | ChemComp-CA / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.71 % |
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Crystal grow | Temperature: 293 K / Method: evaporation Details: 0.1M potassium chloride, 0.1M HEPES pH7.5, 15% (w/v) PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 3.86→202.306 Å / Num. obs: 34296 / % possible obs: 91.22 % / Redundancy: 12.83 % / Biso Wilson estimate: 80.18 Å2 / CC1/2: 0.9932 / Net I/σ(I): 6.187 |
Reflection shell | Resolution: 3.86→4.046 Å / Num. unique obs: 1716 / CC1/2: 0.446 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.86→52.09 Å / Cross valid method: FREE R-VALUE /
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Refinement step | Cycle: LAST / Resolution: 3.86→52.09 Å
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