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Open data
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Basic information
Entry | Database: PDB / ID: 8gs4 | ||||||
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Title | Cryo-EM structure of human Neuroligin 2 | ||||||
![]() | Neuroligin-2 | ||||||
![]() | MEMBRANE PROTEIN / synapse protein / plasma membrane | ||||||
Function / homology | ![]() neurotransmitter-gated ion channel clustering / jump response / positive regulation of t-SNARE clustering / symmetric, GABA-ergic, inhibitory synapse / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / cell-cell junction maintenance / postsynaptic membrane assembly / positive regulation of synaptic vesicle clustering ...neurotransmitter-gated ion channel clustering / jump response / positive regulation of t-SNARE clustering / symmetric, GABA-ergic, inhibitory synapse / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / cell-cell junction maintenance / postsynaptic membrane assembly / positive regulation of synaptic vesicle clustering / presynaptic membrane assembly / thigmotaxis / ribbon synapse / inhibitory synapse / regulation of respiratory gaseous exchange by nervous system process / insulin metabolic process / neuron cell-cell adhesion / presynapse assembly / neurexin family protein binding / dopaminergic synapse / protein localization to synapse / inhibitory synapse assembly / regulation of AMPA receptor activity / positive regulation of inhibitory postsynaptic potential / glycinergic synapse / synaptic transmission, GABAergic / protein localization to cell surface / postsynaptic specialization membrane / Neurexins and neuroligins / positive regulation of synapse assembly / positive regulation of protein localization to synapse / positive regulation of dendritic spine development / locomotory exploration behavior / positive regulation of excitatory postsynaptic potential / social behavior / neuromuscular process controlling balance / regulation of presynapse assembly / synaptic vesicle endocytosis / excitatory synapse / sensory perception of pain / cell adhesion molecule binding / synapse assembly / positive regulation of synaptic transmission, glutamatergic / dendritic shaft / positive regulation of synaptic transmission, GABAergic / synapse organization / modulation of chemical synaptic transmission / positive regulation of insulin secretion / cell-cell adhesion / presynaptic membrane / signaling receptor activity / chemical synaptic transmission / postsynaptic membrane / synapse / positive regulation of cell population proliferation / cell surface / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
![]() | Zhang, H. / Zhang, Z. / Hou, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Expression and structural analysis of human neuroligin 2 and neuroligin 3 implicated in autism spectrum disorders. Authors: Zhenzhen Zhang / Mengzhuo Hou / Huaxing Ou / Daping Wang / Zhifang Li / Huawei Zhang / Jianping Lu / ![]() Abstract: The development of autism spectrum disorders (ASDs) involves both environmental factors such as maternal diabetes and genetic factors such as neuroligins (NLGNs). NLGN2 and NLGN3 are two members of ...The development of autism spectrum disorders (ASDs) involves both environmental factors such as maternal diabetes and genetic factors such as neuroligins (NLGNs). NLGN2 and NLGN3 are two members of NLGNs with distinct distributions and functions in synapse development and plasticity. The relationship between maternal diabetes and NLGNs, and the distinct working mechanisms of different NLGNs currently remain unclear. Here, we first analyzed the expression levels of NLGN2 and NLGN3 in a streptozotocin-induced ASD mouse model and different brain regions to reveal their differences and similarities. Then, cryogenic electron microscopy (cryo-EM) structures of human NLGN2 and NLGN3 were determined. The overall structures are similar to their homologs in previous reports. However, structural comparisons revealed the relative rotations of two protomers in the homodimers of NLGN2 and NLGN3. Taken together with the previously reported NLGN2-MDGA1 complex, we speculate that the distinct assembly adopted by NLGN2 and NLGN3 may affect their interactions with MDGAs. Our results provide structural insights into the potential distinct mechanisms of NLGN2 and NLGN3 implicated in the development of ASD. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.2 KB | Display | ![]() |
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PDB format | ![]() | 153.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 39.9 KB | Display | |
Data in CIF | ![]() | 57.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 34220MC ![]() 8gs3C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 90913.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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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 |
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Sample preparation
Component | Name: homodimer of Neuroligin 2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: dev_3951: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192341 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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