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- PDB-8gs4: Cryo-EM structure of human Neuroligin 2 -

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Basic information

Entry
Database: PDB / ID: 8gs4
TitleCryo-EM structure of human Neuroligin 2
ComponentsNeuroligin-2
KeywordsMEMBRANE PROTEIN / synapse protein / plasma membrane
Function / homology
Function and homology information


symmetric, GABA-ergic, inhibitory synapse / jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / positive regulation of synaptic vesicle clustering / postsynaptic membrane assembly / cell-cell junction maintenance ...symmetric, GABA-ergic, inhibitory synapse / jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / positive regulation of synaptic vesicle clustering / postsynaptic membrane assembly / cell-cell junction maintenance / presynaptic membrane assembly / neurexin family protein binding / presynapse assembly / thigmotaxis / neuron cell-cell adhesion / insulin metabolic process / regulation of respiratory gaseous exchange by nervous system process / inhibitory synapse / ribbon synapse / protein localization to synapse / dopaminergic synapse / positive regulation of inhibitory postsynaptic potential / glycinergic synapse / inhibitory synapse assembly / protein localization to cell surface / positive regulation of synapse assembly / Neurexins and neuroligins / postsynaptic specialization membrane / neuromuscular process controlling balance / positive regulation of protein localization to synapse / synaptic transmission, GABAergic / positive regulation of dendritic spine development / locomotory exploration behavior / excitatory synapse / social behavior / positive regulation of excitatory postsynaptic potential / regulation of presynapse assembly / positive regulation of synaptic transmission, glutamatergic / synapse assembly / cell adhesion molecule binding / sensory perception of pain / dendritic shaft / positive regulation of synaptic transmission, GABAergic / cell-cell adhesion / positive regulation of insulin secretion / synapse organization / modulation of chemical synaptic transmission / presynaptic membrane / postsynaptic membrane / axon / positive regulation of cell population proliferation / synapse / cell surface / identical protein binding / membrane / plasma membrane
Similarity search - Function
Neuroligin / : / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang, H. / Zhang, Z. / Hou, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Front Endocrinol (Lausanne) / Year: 2022
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
DepositionSep 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
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Revision 1.1Apr 3, 2024Group: Data collection / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / em_author_list
Item: _audit_author.name / _em_author_list.author
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
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Revision 1.3Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuroligin-2
B: Neuroligin-2


Theoretical massNumber of molelcules
Total (without water)181,8282
Polymers181,8282
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Neuroligin-2


Mass: 90913.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLGN2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8NFZ4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: homodimer of Neuroligin 2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_3951: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192341 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048482
ELECTRON MICROSCOPYf_angle_d0.79211554
ELECTRON MICROSCOPYf_dihedral_angle_d6.8261140
ELECTRON MICROSCOPYf_chiral_restr0.0481236
ELECTRON MICROSCOPYf_plane_restr0.0071518

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