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

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Basic information

Entry
Database: PDB / ID: 6cmx
TitleHuman Teneurin 2 extra-cellular region
ComponentsTeneurin-2
KeywordsMEMBRANE PROTEIN / Teneurin / Membrane protein / CNS
Function / homologyTeneurin Intracellular Region / EGF-like domain signature 2. / YD repeat / Carboxypeptidase-like, regulatory domain superfamily / GHH signature containing HNH/Endo VII superfamily nuclease toxin / Teneurin intracellular, N-terminal / EGF-like domain signature 1. / EGF-like calcium-binding domain / Quinoprotein amine dehydrogenase, beta chain-like / Six-bladed beta-propeller, TolB-like ...Teneurin Intracellular Region / EGF-like domain signature 2. / YD repeat / Carboxypeptidase-like, regulatory domain superfamily / GHH signature containing HNH/Endo VII superfamily nuclease toxin / Teneurin intracellular, N-terminal / EGF-like domain signature 1. / EGF-like calcium-binding domain / Quinoprotein amine dehydrogenase, beta chain-like / Six-bladed beta-propeller, TolB-like / EGF-like domain / EGF-like domain profile. / Tox-GHH domain / Teneurin N-terminal domain profile. / Rhs repeat-associated core / Teneurin-2/3 / EGF-like, conserved site / 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 / calcium-mediated signaling using intracellular calcium source / filopodium / cell adhesion molecule binding / cell-cell adhesion / PML body / postsynaptic membrane / cell-cell junction / axon guidance / growth cone / dendritic spine / cell junction / neuron projection / synapse / dendrite / signaling receptor binding / calcium ion binding / protein heterodimerization activity / endoplasmic reticulum / integral component of plasma membrane / Golgi apparatus / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / plasma membrane / nucleus / Teneurin-2
Function and homology information
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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Structure visualization

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Assembly

Deposited unit
A: Teneurin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,52018
Polyers224,0061
Non-polymers3,51417
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#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 / References: UniProt: Q9NT68*PLUS
#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 11 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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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

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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)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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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