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- PDB-8g7y: Cryo-EM Structure of full length Neuroligin-2 from mouse with Neu... -

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Basic information

Entry
Database: PDB / ID: 8g7y
TitleCryo-EM Structure of full length Neuroligin-2 from mouse with Neurexin-1 beta
Components
  • Neurexin-1
  • Neuroligin-2
KeywordsMEMBRANE PROTEIN / Neuroligin-2 / Neurexin-1 beta
Function / homology
Function and homology information


jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / Neurexins and neuroligins / positive regulation of synaptic vesicle clustering ...jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / Neurexins and neuroligins / positive regulation of synaptic vesicle clustering / presynaptic membrane assembly / neurexin family protein binding / thigmotaxis / presynapse assembly / cell adhesion mediator activity / neuron cell-cell adhesion / regulation of respiratory gaseous exchange by nervous system process / insulin metabolic process / ribbon synapse / inhibitory synapse / protein localization to synapse / dopaminergic synapse / glycinergic synapse / neurotransmitter secretion / protein localization to cell surface / inhibitory synapse assembly / positive regulation of synapse assembly / positive regulation of inhibitory postsynaptic potential / neuromuscular process controlling balance / postsynaptic specialization membrane / positive regulation of protein localization to synapse / synaptic transmission, GABAergic / positive regulation of dendritic spine development / locomotory exploration behavior / social behavior / regulation of presynapse assembly / positive regulation of synaptic transmission, glutamatergic / synapse assembly / cell adhesion molecule binding / excitatory synapse / sensory perception of pain / positive regulation of excitatory postsynaptic potential / dendritic shaft / positive regulation of synaptic transmission, GABAergic / calcium channel regulator activity / synapse organization / modulation of chemical synaptic transmission / GABA-ergic synapse / positive regulation of insulin secretion / presynaptic membrane / postsynaptic membrane / cell adhesion / axon / positive regulation of cell population proliferation / synapse / dendrite / glutamatergic synapse / cell surface / identical protein binding / plasma membrane
Similarity search - Function
Syndecan/Neurexin domain / Syndecan domain / Neuroligin / : / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / Laminin G domain / Laminin G domain profile. / Laminin G domain ...Syndecan/Neurexin domain / Syndecan domain / Neuroligin / : / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Neurexin I / Neuroligin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsBoyd, R. / Wang, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R35Gm146860 United States
Other private2022 Scholar Award
CitationJournal: Sci Adv / Year: 2026
Title: Weaker neuroligin 2-neurexin β1 interaction tethers membranes and recruits gephyrin at membrane junctions through clustering.
Authors: Robbie Boyd / Khuloud Jaqaman / Weiwei Wang /
Abstract: Single-pass transmembrane proteins neuroligin (NL) and neurexin (NRX) constitute a pair of synaptic adhesion molecules that are essential for the formation of functional synapses. Binding affinities ...Single-pass transmembrane proteins neuroligin (NL) and neurexin (NRX) constitute a pair of synaptic adhesion molecules that are essential for the formation of functional synapses. Binding affinities vary by ~1000-fold between combinations of NL and NRX subtypes, which contribute to chemical and spatial specificities. Among major NL-NRX subtypes, NL2 and NRXβ1 have the lowest affinity. Here, we report structures of NL2 in complex with NRXβ1 in several conformations, along with NL2 alone. We identify mechanisms underlying the modulation of NL-NRX affinities and how the weaker NL2-NRXβ1 interaction alone is capable of tethering lipid membranes. We further show that NL2 and NRXβ1 cluster at intercellular junctions and recruit the master postsynaptic scaffolding protein gephyrin, which further clusters neurotransmitter receptors. These findings suggest a dual role of the NL2-NRXβ1 interaction-both as mechanical tether and as signaling receptor-to ensure correct spatial and chemical coordination between two cells to generate functional synapses.
History
DepositionFeb 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
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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
C: Neurexin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,0179
Polymers239,8713
Non-polymers1,1466
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: 95226.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nlgn2 / Production host: Homo sapiens (human) / References: UniProt: Q62888
#2: Protein Neurexin-1


Mass: 49417.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nrxn1 / Production host: Homo sapiens (human) / References: UniProt: E0CZA5
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Neuroligin-2 Dimer bound to one Neurexin-1 beta / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMSodium ChlorideNaCl1
31 mMMagnesium ChlorideMgCl21
40.5 mMCalcium ChlorideCaCl1
50.05 %LMNG1
SpecimenConc.: 6.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: Blot force 20, blot time 5s, single blot

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus max: 3600 nm / Cs: 0 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 90 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6615
Image scansWidth: 5760 / Height: 4092

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2964465
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46435 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 3BLB

3blb


Accession code: 3BLB / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310039
ELECTRON MICROSCOPYf_angle_d0.51313684
ELECTRON MICROSCOPYf_dihedral_angle_d4.311394
ELECTRON MICROSCOPYf_chiral_restr0.0411504
ELECTRON MICROSCOPYf_plane_restr0.0041790

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