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- PDB-6cmx: Human Teneurin 2 extra-cellular region -

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Basic information

Database: PDB / ID: 6cmx
TitleHuman Teneurin 2 extra-cellular region
KeywordsMEMBRANE PROTEIN / Teneurin / Membrane protein / CNS
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.1 Å resolution
AuthorsShalev-Benami, M. / Li, J. / Sudhof, T. / Skiniotis, G. / Arac, D.
CitationJournal: 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 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 6, 2018 / Release: Jul 25, 2018

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Deposited unit
A: Teneurin-2
hetero molecules

Theoretical massNumber of molelcules
Total (without water)227,52018

TypeNameSymmetry operationNumber
identity operation1_5551


#1: Protein/peptide Teneurin-2 / Ten-2 / Protein Odd Oz/ten-m homolog 2 / Tenascin-M2 / Ten-m2 / Teneurin transmembrane protein 2

Mass: 224005.812 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: TENM2, KIAA1127, ODZ2, TNM2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High-Five
#2: Chemical

Mass: 221.208 Da / Num. of mol.: 11 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical

Mass: 180.156 Da / Num. of mol.: 6 / Formula: C6H12O6

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

ComponentName: Teneurin 2 extra-cellular region / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.215 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298.15 kelvins

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 426107 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00910387
ELECTRON MICROSCOPYf_angle_d1.22714140
ELECTRON MICROSCOPYf_dihedral_angle_d14.8025937
ELECTRON MICROSCOPYf_chiral_restr0.1381623
ELECTRON MICROSCOPYf_plane_restr0.0121772

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